1-158382610-T-G

Position:

• chr1-158382610-T-G

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 0.355 in 151,690 control chromosomes in the GnomAD database, including 11,864 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 0.36 (11864 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.158382610T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53754 AN: 151572 Hom.: 11822 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.355 AC: 53860 AN: 151690 Hom.: 11864 Cov.: 32 AF XY: 0.355 AC XY: 26340 AN XY: 74144

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.307

Alfa AF: 0.226 Hom.: 1080

Bravo AF: 0.362

Asia WGS AF: 0.339 AC: 1178 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11264965; hg19: chr1-158352400;