rs7328507

chr13-38448054-T-Cchr13-38448054-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.527

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.8
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

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