13-71409209-A-G

Variant names:

• chr13-71409209-A-G
• rs1999603

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 0.793 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
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.545 AC: 22577 AN: 41440

American (AMR) AF: 0.852 AC: 12982 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4300 AN: 5164

South Asian (SAS) AF: 0.884 AC: 4245 AN: 4800

European-Finnish (FIN) AF: 0.938 AC: 9958 AN: 10612

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60603 AN: 67948

Other (OTH) AF: 0.809 AC: 1695 AN: 2096

Alfa AF: 0.856 Hom.: 176024

Bravo AF: 0.775

Asia WGS AF: 0.837 AC: 2910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.50
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs1999603; hg19: chr13-71983341;