rs1937506

Variant names:

• chr13-67461239-G-A
• rs1937506

Your query was ambiguous. Multiple possible variants found:

• chr13-67461239-G-A
• chr13-67461239-G-C

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 0.255 in 150,280 control chromosomes in the GnomAD database, including 5,079 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 0.25 (5079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 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: 0.255 AC: 38240 AN: 150162 Hom.: 5074 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.255 AC: 38278 AN: 150280 Hom.: 5079 Cov.: 32 AF XY: 0.261 AC XY: 19126 AN XY: 73364

African (AFR) AF: 0.186 AC: 7592 AN: 40778

American (AMR) AF: 0.304 AC: 4539 AN: 14948

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 940 AN: 3458

East Asian (EAS) AF: 0.151 AC: 759 AN: 5040

South Asian (SAS) AF: 0.302 AC: 1419 AN: 4696

European-Finnish (FIN) AF: 0.390 AC: 4064 AN: 10432

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18251 AN: 67654

Other (OTH) AF: 0.236 AC: 490 AN: 2074

Alfa AF: 0.253 Hom.: 6436

Bravo AF: 0.239

Asia WGS AF: 0.260 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1937506; hg19: chr13-68035371;