rs7328410

Variant names:

• chr13-105373851-T-G
• rs7328410

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 0.129 in 152,112 control chromosomes in the GnomAD database, including 2,012 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 0.13 (2012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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: 0.129 AC: 19568 AN: 151994 Hom.: 2004 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0477

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.129 AC: 19617 AN: 152112 Hom.: 2012 Cov.: 32 AF XY: 0.129 AC XY: 9623 AN XY: 74354

African (AFR) AF: 0.260 AC: 10799 AN: 41458

American (AMR) AF: 0.201 AC: 3067 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0789 AC: 274 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5170

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4824

European-Finnish (FIN) AF: 0.0477 AC: 505 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0444 AC: 3019 AN: 67996

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.0722 Hom.: 1239

Bravo AF: 0.150

Asia WGS AF: 0.153 AC: 533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.60
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7328410; hg19: chr13-106026201;