rs1932064

chr1-70608238-A-G

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 0.134 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

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 (EAS) allele frequency at 95% confidence interval = 0.252 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: 0.134 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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0774

Gnomad4 NFE AF: 0.0743

Gnomad4 OTH AF: 0.112

Alfa AF: 0.102 Hom.: 487

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1932064; hg19: chr1-71073921;