13-71409209-A-G

Variant names:

• chr13-71409209-A-G
• rs1999603

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.793 in 151,978 control chromosomes in the GnomAD database, including 49,730 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 0.79 (49730 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 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: 0.793 AC: 120485 AN: 151862 Hom.: 49713 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.793 AC: 120531 AN: 151978 Hom.: 49730 Cov.: 31 AF XY: 0.798 AC XY: 59296 AN XY: 74294

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.809

Alfa AF: 0.877 Hom.: 114539

Bravo AF: 0.775

Asia WGS AF: 0.837 AC: 2910 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	1.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999603; hg19: chr13-71983341;