chr13-39997933-T-G

Variant names:

• chr13-39997933-T-G
• rs276420
• ENST00000837163.1:n.584A>C

Variant summary

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

The ENST00000837163.1(ENSG00000308901):​n.584A>C 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 0.486 in 152,096 control chromosomes in the GnomAD database, including 18,413 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 0.49 (18413 hom., cov: 32)
• Consequence: ENSG00000308901 ENST00000837163.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 7 publications found

Genes affected

ENSG00000308901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837163.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308901	ENST00000837163.1		n.584A>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73852 AN: 151978 Hom.: 18413 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.486 AC: 73866 AN: 152096 Hom.: 18413 Cov.: 32 AF XY: 0.483 AC XY: 35901 AN XY: 74360

African (AFR) AF: 0.418 AC: 17341 AN: 41462

American (AMR) AF: 0.415 AC: 6341 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1947 AN: 5168

South Asian (SAS) AF: 0.600 AC: 2889 AN: 4818

European-Finnish (FIN) AF: 0.470 AC: 4974 AN: 10572

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36586 AN: 68016

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

Alfa AF: 0.521 Hom.: 78246

Bravo AF: 0.473

Asia WGS AF: 0.501 AC: 1745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.78
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs276420; hg19: chr13-40572070;