rs1757387

Variant names:

• chr13-103699561-G-A
• rs1757387

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 0.698 in 152,082 control chromosomes in the GnomAD database, including 37,423 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 0.70 (37423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.698 AC: 106082 AN: 151964 Hom.: 37396 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.698 AC: 106151 AN: 152082 Hom.: 37423 Cov.: 32 AF XY: 0.698 AC XY: 51874 AN XY: 74340

African (AFR) AF: 0.598 AC: 24810 AN: 41458

American (AMR) AF: 0.732 AC: 11192 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2783 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4233 AN: 5174

South Asian (SAS) AF: 0.794 AC: 3824 AN: 4816

European-Finnish (FIN) AF: 0.654 AC: 6914 AN: 10570

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49900 AN: 67998

Other (OTH) AF: 0.743 AC: 1568 AN: 2110

Alfa AF: 0.733 Hom.: 70967

Bravo AF: 0.698

Asia WGS AF: 0.779 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.35
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1757387; hg19: chr13-104351911;