rs3909263

Variant names:

• chr13-72281083-G-C
• rs3909263

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 0.323 in 151,866 control chromosomes in the GnomAD database, including 8,380 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 0.32 (8380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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: 0.323 AC: 48979 AN: 151748 Hom.: 8374 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.323 AC: 49020 AN: 151866 Hom.: 8380 Cov.: 32 AF XY: 0.320 AC XY: 23748 AN XY: 74248

African (AFR) AF: 0.410 AC: 16959 AN: 41404

American (AMR) AF: 0.386 AC: 5888 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3466

East Asian (EAS) AF: 0.144 AC: 742 AN: 5158

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2678 AN: 10546

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20072 AN: 67922

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.309 Hom.: 946

Bravo AF: 0.335

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3909263; hg19: chr13-72855221;