chr13-38448054-T-C

Variant names:

• chr13-38448054-T-C
• rs7328507

Variant summary

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

The variant allele was found at a frequency of 0.545 in 152,000 control chromosomes in the GnomAD database, including 23,908 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 0.55 (23908 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82877 AN: 151882 Hom.: 23904 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.545 AC: 82893 AN: 152000 Hom.: 23908 Cov.: 32 AF XY: 0.544 AC XY: 40435 AN XY: 74286

African (AFR) AF: 0.401 AC: 16607 AN: 41412

American (AMR) AF: 0.504 AC: 7700 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1622 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4818

European-Finnish (FIN) AF: 0.734 AC: 7749 AN: 10558

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44097 AN: 67988

Other (OTH) AF: 0.527 AC: 1112 AN: 2110

Alfa AF: 0.601 Hom.: 3773

Bravo AF: 0.523

Asia WGS AF: 0.358 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7328507; hg19: chr13-39022191; COSMIC: COSV69347481;