13-37157982-C-T

Variant names:

• chr13-37157982-C-T
• rs7327020
• ENST00000827668.1:n.232+2258C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827668.1(ENSG00000307651):​n.232+2258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 150,798 control chromosomes in the GnomAD database, including 35,891 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 0.66 (35891 hom., cov: 29)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307651	ENST00000827668.1	n.232+2258C>T		intron_variant	Intron 1 of 2
ENSG00000307674	ENST00000827784.1	n.353-29189C>T		intron_variant	Intron 3 of 4
ENSG00000307674	ENST00000827785.1	n.196-29189C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.656 AC: 98938 AN: 150730 Hom.: 35892 Cov.: 29

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.677

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.656 AC: 98950 AN: 150798 Hom.: 35891 Cov.: 29 AF XY: 0.665 AC XY: 48967 AN XY: 73634

African (AFR) AF: 0.318 AC: 12952 AN: 40694

American (AMR) AF: 0.715 AC: 10851 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2470 AN: 3466

East Asian (EAS) AF: 0.956 AC: 4908 AN: 5136

South Asian (SAS) AF: 0.820 AC: 3938 AN: 4804

European-Finnish (FIN) AF: 0.836 AC: 8621 AN: 10314

Middle Eastern (MID) AF: 0.656 AC: 189 AN: 288

European-Non Finnish (NFE) AF: 0.778 AC: 52859 AN: 67914

Other (OTH) AF: 0.678 AC: 1425 AN: 2102

Alfa AF: 0.680 Hom.: 5080

Bravo AF: 0.627

Asia WGS AF: 0.842 AC: 2927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7327020; hg19: chr13-37732119;