1-152618666-A-C

Position:

• chr1-152618666-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 0.58 in 152,066 control chromosomes in the GnomAD database, including 26,256 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 0.58 (26256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 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: 0.580 AC: 88086 AN: 151948 Hom.: 26249 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.580 AC: 88127 AN: 152066 Hom.: 26256 Cov.: 32 AF XY: 0.584 AC XY: 43436 AN XY: 74330

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.582

Alfa AF: 0.612 Hom.: 12956

Bravo AF: 0.567

Asia WGS AF: 0.582 AC: 2025 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	0.73
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886734; hg19: chr1-152591142;