chr1-179016523-T-C

Variant names:

• chr1-179016523-T-C
• rs4271171

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 0.551 in 151,984 control chromosomes in the GnomAD database, including 24,729 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 0.55 (24729 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.551 AC: 83718 AN: 151864 Hom.: 24692 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.551 AC: 83811 AN: 151984 Hom.: 24729 Cov.: 31 AF XY: 0.550 AC XY: 40859 AN XY: 74280

African (AFR) AF: 0.768 AC: 31814 AN: 41450

American (AMR) AF: 0.468 AC: 7148 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1591 AN: 5152

South Asian (SAS) AF: 0.472 AC: 2275 AN: 4824

European-Finnish (FIN) AF: 0.528 AC: 5576 AN: 10554

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31875 AN: 67934

Other (OTH) AF: 0.557 AC: 1178 AN: 2114

Alfa AF: 0.514 Hom.: 5884

Bravo AF: 0.557

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.37
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs4271171; hg19: chr1-178985658;