rs9541712

Variant names:

• chr13-69009607-A-C
• rs9541712

Your query was ambiguous. Multiple possible variants found:

• chr13-69009607-A-C
• chr13-69009607-A-T

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 0.647 in 151,846 control chromosomes in the GnomAD database, including 32,076 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 0.65 (32076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 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: 0.647 AC: 98242 AN: 151728 Hom.: 32057 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.721

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.647 AC: 98299 AN: 151846 Hom.: 32076 Cov.: 32 AF XY: 0.647 AC XY: 48052 AN XY: 74216

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.650

Alfa AF: 0.661 Hom.: 10593

Bravo AF: 0.635

Asia WGS AF: 0.644 AC: 2214 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9541712; hg19: chr13-69583739;