1-60320574-A-G

Variant names:

• chr1-60320574-A-G
• rs169872

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 0.417 in 151,728 control chromosomes in the GnomAD database, including 13,893 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 0.42 (13893 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.417 AC: 63210 AN: 151614 Hom.: 13874 Cov.: 30

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.417 AC: 63252 AN: 151728 Hom.: 13893 Cov.: 30 AF XY: 0.422 AC XY: 31314 AN XY: 74132

African (AFR) AF: 0.357 AC: 14777 AN: 41384

American (AMR) AF: 0.476 AC: 7259 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4126 AN: 5108

South Asian (SAS) AF: 0.619 AC: 2977 AN: 4808

European-Finnish (FIN) AF: 0.399 AC: 4188 AN: 10500

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27038 AN: 67910

Other (OTH) AF: 0.447 AC: 942 AN: 2106

Alfa AF: 0.406 Hom.: 4844

Bravo AF: 0.418

Asia WGS AF: 0.671 AC: 2330 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.28
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs169872; hg19: chr1-60786246;