chr1-158346134-G-T

Position:

• chr1-158346134-G-T

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 0.118 in 152,138 control chromosomes in the GnomAD database, including 1,417 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 0.12 (1417 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17995 AN: 152020 Hom.: 1418 Cov.: 31

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.118 AC: 17995 AN: 152138 Hom.: 1417 Cov.: 31 AF XY: 0.122 AC XY: 9079 AN XY: 74376

Gnomad4 AFR AF: 0.0537

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.119

Alfa AF: 0.127 Hom.: 1594

Bravo AF: 0.115

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317955; hg19: chr1-158315924;