rs1225130

Positions:

• chr11-76840204-G-C

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 0.561 in 152,032 control chromosomes in the GnomAD database, including 25,498 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 0.56 (25498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.561 AC: 85164 AN: 151914 Hom.: 25461 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.561 AC: 85251 AN: 152032 Hom.: 25498 Cov.: 32 AF XY: 0.565 AC XY: 41984 AN XY: 74286

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.555

Alfa AF: 0.527 Hom.: 2067

Bravo AF: 0.574

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1225130; hg19: chr11-76551248;