1-232041741-G-A

Variant names:

• chr1-232041741-G-A
• rs1411776

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 0.138 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.104 AC: 4318 AN: 41476

American (AMR) AF: 0.118 AC: 1808 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3468

East Asian (EAS) AF: 0.136 AC: 705 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4828

European-Finnish (FIN) AF: 0.129 AC: 1362 AN: 10576

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10969 AN: 67966

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.152 Hom.: 1657

Bravo AF: 0.132

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1411776; hg19: chr1-232177487;