chr1-161310673-G-A

Variant names:

• chr1-161310673-G-A
• rs12064957

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 0.0949 in 152,226 control chromosomes in the GnomAD database, including 846 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 0.095 (846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0949 AC: 14434 AN: 152108 Hom.: 845 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0595

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0949 AC: 14449 AN: 152226 Hom.: 846 Cov.: 32 AF XY: 0.0970 AC XY: 7219 AN XY: 74434

African (AFR) AF: 0.138 AC: 5737 AN: 41526

American (AMR) AF: 0.0953 AC: 1457 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.168 AC: 871 AN: 5186

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4822

European-Finnish (FIN) AF: 0.0328 AC: 348 AN: 10606

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0637 AC: 4329 AN: 68008

Other (OTH) AF: 0.111 AC: 235 AN: 2112

Alfa AF: 0.0792 Hom.: 739

Bravo AF: 0.0993

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.58
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs12064957; hg19: chr1-161280463;