13-103536717-A-G

Variant names:

• chr13-103536717-A-G
• rs1121605

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 0.727 in 152,068 control chromosomes in the GnomAD database, including 41,030 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 0.73 (41030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 1 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 = 0.815 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: 0.727 AC: 110472 AN: 151950 Hom.: 41010 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.727 AC: 110539 AN: 152068 Hom.: 41030 Cov.: 32 AF XY: 0.720 AC XY: 53489 AN XY: 74306

African (AFR) AF: 0.635 AC: 26332 AN: 41470

American (AMR) AF: 0.827 AC: 12643 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2907 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2808 AN: 5156

South Asian (SAS) AF: 0.720 AC: 3473 AN: 4824

European-Finnish (FIN) AF: 0.588 AC: 6223 AN: 10578

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53801 AN: 67980

Other (OTH) AF: 0.753 AC: 1585 AN: 2104

Alfa AF: 0.739 Hom.: 5081

Bravo AF: 0.744

Asia WGS AF: 0.615 AC: 2143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.40
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1121605; hg19: chr13-104189067;