rs1329444

Variant names:

• chr1-195263882-C-A
• rs1329444

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 0.668 in 151,974 control chromosomes in the GnomAD database, including 34,530 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 0.67 (34530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.668 AC: 101385 AN: 151856 Hom.: 34487 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.668 AC: 101482 AN: 151974 Hom.: 34530 Cov.: 32 AF XY: 0.668 AC XY: 49622 AN XY: 74270

African (AFR) AF: 0.806 AC: 33428 AN: 41498

American (AMR) AF: 0.712 AC: 10869 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3033 AN: 5162

South Asian (SAS) AF: 0.661 AC: 3187 AN: 4818

European-Finnish (FIN) AF: 0.560 AC: 5888 AN: 10522

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40944 AN: 67928

Other (OTH) AF: 0.670 AC: 1416 AN: 2114

Alfa AF: 0.653 Hom.: 4546

Bravo AF: 0.687

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.34
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1329444; hg19: chr1-195233012; COSMIC: COSV60010175;