rs1323690

Positions:

• chr11-34479140-G-A
• chr11-34479140-G-C
• chr11-34479140-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ELF5	NM_001422.4	c.*1078C>T		3_prime_UTR_variant	7/7	ENST00000257832.7	NP_001413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELF5	ENST00000257832.7	c.*1078C>T		3_prime_UTR_variant	7/7	1	NM_001422.4	ENSP00000257832	P1
ELF5	ENST00000312319.6	c.*1078C>T		3_prime_UTR_variant	7/7	1		ENSP00000311010
ELF5	ENST00000620316.4	c.*1078C>T		3_prime_UTR_variant	6/6	5		ENSP00000484521

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51256 AN: 151992 Hom.: 9265 Cov.: 34

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.: 19 Cov.: 0 AF XY: 0.235 AC XY: 61 AN XY: 260

Gnomad4 FIN exome AF: 0.239

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.337 AC: 51272 AN: 152110 Hom.: 9271 Cov.: 34 AF XY: 0.338 AC XY: 25102 AN XY: 74354

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.394

Alfa AF: 0.384 Hom.: 22076

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
DANN	Benign	0.58

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

LitVar

Other links and lift over

dbSNP: rs1323690; hg19: chr11-34500687; COSMIC: COSV56629106; COSMIC: COSV56629106;