chr1-181823356-G-A

Position:

• chr1-181823356-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;