13-37476314-C-T

Variant names:

• chr13-37476314-C-T
• rs7323534
• ENST00000827669.1:n.223-2291C>T

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.223-2291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,968 control chromosomes in the GnomAD database, including 15,048 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 0.42 (15048 hom., cov: 33)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827669.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307651	ENST00000827669.1		n.223-2291C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62989 AN: 151850 Hom.: 15015 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.415 AC: 63075 AN: 151968 Hom.: 15048 Cov.: 33 AF XY: 0.417 AC XY: 31003 AN XY: 74304

African (AFR) AF: 0.647 AC: 26819 AN: 41452

American (AMR) AF: 0.427 AC: 6511 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2572 AN: 5160

South Asian (SAS) AF: 0.558 AC: 2687 AN: 4812

European-Finnish (FIN) AF: 0.248 AC: 2613 AN: 10554

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19434 AN: 67940

Other (OTH) AF: 0.407 AC: 860 AN: 2114

Alfa AF: 0.348 Hom.: 1267

Bravo AF: 0.436

Asia WGS AF: 0.545 AC: 1895 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.58
PhyloP100		0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7323534;

hg19: chr13-38050451;

COSMIC: COSV69347236;