Genetic Variant NM_001422.4:c.*1078C>T (chr11-34479140-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001422.4(ELF5):c.*1078C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,544 control chromosomes in the GnomAD database, including 9,290 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9271 hom., cov: 34)

Exomes 𝑓: 0.24 ( 19 hom. )

Consequence

ELF5
NM_001422.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0760

Publications

16 publications found

Variant links:

Genes affected

ELF5 (HGNC:3320): (E74 like ETS transcription factor 5) This gene encodes an epithelium-specific ETS family transcription factor. In addition to its role in regulating the later stages of terminal differentiation of keratinocytes, it appears to regulate a number of epithelium-specific genes found in tissues containing glandular epithelium such as salivary gland and prostate. It has very low affinity to DNA due to its negative regulatory domain at the amino terminus. This gene has been implicated as a tumor suppressive transcription factor in breast cancer. [provided by RefSeq, May 2022]

ELF5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF5	NM_001422.4 link	c.*1078C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000257832.7	NP_001413.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ELF5	ENST00000257832.7 link	c.*1078C>T	3_prime_UTR_variant	Exon 7 of 7	1	NM_001422.4	ENSP00000257832.3
ELF5	ENST00000312319.6 link	c.*1078C>T	3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000311010.2
ELF5	ENST00000620316.4 link	c.*1078C>T	3_prime_UTR_variant	Exon 6 of 6	5		ENSP00000484521.1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51256

AN:

151992

Hom.:

9265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.416

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.374

Gnomad OTH

AF:

0.394

GnomAD4 exome

AF:

0.237

AC:

103

AN:

434

Hom.:

Cov.:

AF XY:

0.235

AC XY:

AN XY:

260

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.239

AC:

102

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.337

AC:

51272

AN:

152110

Hom.:

9271

Cov.:

AF XY:

0.338

AC XY:

25102

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.221

AC:

9176

AN:

41492

American (AMR)

AF:

0.454

AC:

6945

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1418

AN:

3470

East Asian (EAS)

AF:

0.419

AC:

2171

AN:

5180

South Asian (SAS)

AF:

0.495

AC:

2389

AN:

4824

European-Finnish (FIN)

AF:

0.229

AC:

2420

AN:

10562

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.374

AC:

25439

AN:

67982

Other (OTH)

AF:

0.394

AC:

832

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1730

3460

5190

6920

8650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.379

Hom.:

29625

Bravo

AF:

0.349

Asia WGS

AF:

0.449

AC:

1564

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.2

(source)

DANN

Benign

0.58

PhyloP100

0.076

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over