chr1-160579933-C-T

Variant names:

• chr1-160579933-C-T
• rs977019

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 0.484 in 151,288 control chromosomes in the GnomAD database, including 19,866 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 0.48 (19866 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73251 AN: 151176 Hom.: 19854 Cov.: 29

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.484 AC: 73285 AN: 151288 Hom.: 19866 Cov.: 29 AF XY: 0.490 AC XY: 36182 AN XY: 73880

African (AFR) AF: 0.229 AC: 9449 AN: 41196

American (AMR) AF: 0.460 AC: 6965 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1946 AN: 3464

East Asian (EAS) AF: 0.658 AC: 3379 AN: 5134

South Asian (SAS) AF: 0.544 AC: 2615 AN: 4804

European-Finnish (FIN) AF: 0.685 AC: 7140 AN: 10420

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40100 AN: 67820

Other (OTH) AF: 0.472 AC: 986 AN: 2090

Alfa AF: 0.559 Hom.: 11360

Bravo AF: 0.457

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.67
PhyloP100		-2.5
PromoterAI		0.00090	Neutral

Splicing

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

Other links and lift over

dbSNP: rs977019; hg19: chr1-160549723;