rs11771570

chr7-131976170-G-Achr7-131976170-G-Cchr7-131976170-G-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 0.9 in 152,258 control chromosomes in the GnomAD database, including 61,939 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 0.90 (61939 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136862 AN: 152140 Hom.: 61872 Cov.: 33

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.900 AC: 136987 AN: 152258 Hom.: 61939 Cov.: 33 AF XY: 0.903 AC XY: 67182 AN XY: 74436

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.901

Alfa AF: 0.884 Hom.: 7574

Bravo AF: 0.904

Asia WGS AF: 0.978 AC: 3400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.69
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11771570; hg19: chr7-131660929;