rs1281194

Variant names:

• chr1-181823356-G-A
• rs1281194

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 0.618 in 151,776 control chromosomes in the GnomAD database, including 29,637 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 0.62 (29637 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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: 0.618 AC: 93772 AN: 151658 Hom.: 29603 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.618 AC: 93858 AN: 151776 Hom.: 29637 Cov.: 31 AF XY: 0.615 AC XY: 45602 AN XY: 74164

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.649

Alfa AF: 0.673 Hom.: 16431

Bravo AF: 0.611

Asia WGS AF: 0.551 AC: 1913 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1281194; hg19: chr1-181792491;