1-11886332-G-A

Variant names:

• chr1-11886332-G-A
• rs4304595

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 0.395 in 151,992 control chromosomes in the GnomAD database, including 12,649 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 0.39 (12649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.395 AC: 59931 AN: 151874 Hom.: 12627 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.395 AC: 60003 AN: 151992 Hom.: 12649 Cov.: 32 AF XY: 0.401 AC XY: 29772 AN XY: 74298

African (AFR) AF: 0.511 AC: 21177 AN: 41430

American (AMR) AF: 0.357 AC: 5452 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2498 AN: 5158

South Asian (SAS) AF: 0.419 AC: 2020 AN: 4820

European-Finnish (FIN) AF: 0.469 AC: 4954 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22023 AN: 67966

Other (OTH) AF: 0.380 AC: 801 AN: 2108

Alfa AF: 0.377 Hom.: 1722

Bravo AF: 0.389

Asia WGS AF: 0.477 AC: 1660 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	0.38
DANN	Benign	0.46
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4304595; hg19: chr1-11946389;