1-175150943-A-C

Position:

• chr1-175150943-A-C

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 0.386 in 151,900 control chromosomes in the GnomAD database, including 11,923 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 0.39 (11923 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58572 AN: 151780 Hom.: 11920 Cov.: 31

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.386 AC: 58599 AN: 151900 Hom.: 11923 Cov.: 31 AF XY: 0.384 AC XY: 28482 AN XY: 74246

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.0939

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.374

Alfa AF: 0.408 Hom.: 20227

Bravo AF: 0.367

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6701037; hg19: chr1-175120079;