Genetic Variant ENSG00000297879:n.89G>T (chr19-49255975-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000751527.1(ENSG00000297879):n.89G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,132 control chromosomes in the GnomAD database, including 18,901 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 0.50 ( 18865 hom., cov: 31)

Exomes 𝑓: 0.51 ( 36 hom. )

Consequence

ENSG00000297879
ENST00000751527.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.63

Publications

6 publications found

Variant links:

Genes affected

ENSG00000297879 (HGNC:):

ENSG00000297879 links:

SLC6A21P (HGNC:31400): (solute carrier family 6 member 21, pseudogene)

SLC6A21P links:

Genome browser will be placed here

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A21P		n.49255975G>T		intragenic_variant
LOC107985340	XR_001753971.2 link	n.467-13428G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000297879	ENST00000751527.1 link	n.89G>T	non_coding_transcript_exon_variant	Exon 2 of 3
SLC6A21P	ENST00000599458.1 link	n.91+37C>A	intron_variant	Intron 1 of 2	6
ENSG00000297851	ENST00000751404.1 link	n.345+38C>A	intron_variant	Intron 2 of 4
ENSG00000297851	ENST00000751405.1 link	n.338+38C>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.496

AC:

75314

AN:

151782

Hom.:

18854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.494

Gnomad OTH

AF:

0.502

GnomAD4 exome

AF:

0.509

AC:

118

AN:

232

Hom.:

Cov.:

AF XY:

0.520

AC XY:

AN XY:

152

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.489

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.483

AC:

AN:

118

Other (OTH)

AF:

0.750

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

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.496

AC:

75363

AN:

151900

Hom.:

18865

Cov.:

AF XY:

0.503

AC XY:

37334

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.434

AC:

18001

AN:

41436

American (AMR)

AF:

0.570

AC:

8684

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.555

AC:

1924

AN:

3468

East Asian (EAS)

AF:

0.627

AC:

3228

AN:

5146

South Asian (SAS)

AF:

0.590

AC:

2837

AN:

4810

European-Finnish (FIN)

AF:

0.511

AC:

5398

AN:

10558

Middle Eastern (MID)

AF:

0.507

AC:

148

AN:

292

European-Non Finnish (NFE)

AF:

0.494

AC:

33548

AN:

67928

Other (OTH)

AF:

0.501

AC:

1055

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1938

3876

5813

7751

9689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<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:

0.447

Hom.:

3483

Bravo

AF:

0.497

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.075

(source)

DANN

Benign

0.60

PhyloP100

-2.6

Splicing

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over