rs11264422

Variant names:

• chr1-155938032-T-A
• rs11264422

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 0.479 in 152,164 control chromosomes in the GnomAD database, including 22,002 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 0.48 (22002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.480 AC: 72965 AN: 152046 Hom.: 22001 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.479 AC: 72958 AN: 152164 Hom.: 22002 Cov.: 32 AF XY: 0.478 AC XY: 35574 AN XY: 74402

African (AFR) AF: 0.118 AC: 4919 AN: 41544

American (AMR) AF: 0.567 AC: 8663 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2243 AN: 3466

East Asian (EAS) AF: 0.161 AC: 833 AN: 5174

South Asian (SAS) AF: 0.540 AC: 2605 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6565 AN: 10578

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45296 AN: 67978

Other (OTH) AF: 0.526 AC: 1113 AN: 2116

Alfa AF: 0.570 Hom.: 3486

Bravo AF: 0.455

Asia WGS AF: 0.334 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.62
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs11264422; hg19: chr1-155907823;