rs1412953

Variant names:

• chr13-103594721-G-A
• rs1412953

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 0.596 in 152,052 control chromosomes in the GnomAD database, including 30,584 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 0.60 (30584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 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: 0.596 AC: 90612 AN: 151934 Hom.: 30584 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.596 AC: 90625 AN: 152052 Hom.: 30584 Cov.: 32 AF XY: 0.597 AC XY: 44382 AN XY: 74312

African (AFR) AF: 0.255 AC: 10583 AN: 41460

American (AMR) AF: 0.742 AC: 11353 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2612 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2885 AN: 5166

South Asian (SAS) AF: 0.597 AC: 2875 AN: 4816

European-Finnish (FIN) AF: 0.718 AC: 7589 AN: 10568

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50635 AN: 67954

Other (OTH) AF: 0.632 AC: 1337 AN: 2116

Alfa AF: 0.709 Hom.: 63409

Bravo AF: 0.589

Asia WGS AF: 0.517 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs1412953; hg19: chr13-104247071;