chr1-190092815-A-T

Position:

• chr1-190092815-A-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 0.182 in 151,434 control chromosomes in the GnomAD database, including 2,674 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 0.18 (2674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 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: 0.182 AC: 27592 AN: 151320 Hom.: 2661 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.216

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.182 AC: 27634 AN: 151434 Hom.: 2674 Cov.: 32 AF XY: 0.186 AC XY: 13769 AN XY: 74020

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.200

Alfa AF: 0.160 Hom.: 257

Bravo AF: 0.181

Asia WGS AF: 0.250 AC: 847 AN: 3384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10920501; hg19: chr1-190061945;