rs7320523

Variant names:

• chr13-68080641-C-T
• rs7320523

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 0.44 in 151,850 control chromosomes in the GnomAD database, including 14,880 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 0.44 (14880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66674 AN: 151732 Hom.: 14852 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.440 AC: 66764 AN: 151850 Hom.: 14880 Cov.: 32 AF XY: 0.441 AC XY: 32769 AN XY: 74230

African (AFR) AF: 0.476 AC: 19716 AN: 41434

American (AMR) AF: 0.366 AC: 5586 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1901 AN: 5148

South Asian (SAS) AF: 0.468 AC: 2251 AN: 4812

European-Finnish (FIN) AF: 0.448 AC: 4723 AN: 10538

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29372 AN: 67890

Other (OTH) AF: 0.411 AC: 866 AN: 2106

Alfa AF: 0.436 Hom.: 7579

Bravo AF: 0.437

Asia WGS AF: 0.437 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.6
DANN	Benign	0.76
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs7320523; hg19: chr13-68654773; COSMIC: COSV69360709;