1-160579933-C-T

Variant names:

• chr1-160579933-C-T
• rs977019

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 0.484 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.472

Alfa AF: 0.561 Hom.: 10054

Bravo AF: 0.457

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977019; hg19: chr1-160549723;