rs1932064

Variant names:

• chr1-70608238-A-G
• rs1932064

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 0.134 in 152,172 control chromosomes in the GnomAD database, including 1,826 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 0.13 (1826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.252 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: 0.134 AC: 20415 AN: 152052 Hom.: 1820 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.134 AC: 20438 AN: 152172 Hom.: 1826 Cov.: 32 AF XY: 0.136 AC XY: 10110 AN XY: 74412

African (AFR) AF: 0.239 AC: 9930 AN: 41472

American (AMR) AF: 0.121 AC: 1851 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1365 AN: 5186

South Asian (SAS) AF: 0.165 AC: 798 AN: 4828

European-Finnish (FIN) AF: 0.0774 AC: 821 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0743 AC: 5051 AN: 67998

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.110 Hom.: 1180

Bravo AF: 0.142

Asia WGS AF: 0.186 AC: 645 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	6.9
DANN	Benign	0.76
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1932064; hg19: chr1-71073921;