chr1-232041741-G-A

Position:

• chr1-232041741-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 0.138 in 152,086 control chromosomes in the GnomAD database, including 1,582 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 0.14 (1582 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 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: 0.138 AC: 20953 AN: 151966 Hom.: 1579 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.138 AC: 20961 AN: 152086 Hom.: 1582 Cov.: 33 AF XY: 0.139 AC XY: 10336 AN XY: 74364

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.141

Alfa AF: 0.153 Hom.: 1443

Bravo AF: 0.132

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411776; hg19: chr1-232177487;