chr1-190092815-A-T

Variant names:

• chr1-190092815-A-T
• rs10920501

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.216 AC: 8951 AN: 41428

American (AMR) AF: 0.163 AC: 2480 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5170

South Asian (SAS) AF: 0.251 AC: 1214 AN: 4830

European-Finnish (FIN) AF: 0.174 AC: 1795 AN: 10298

Middle Eastern (MID) AF: 0.221 AC: 61 AN: 276

European-Non Finnish (NFE) AF: 0.157 AC: 10618 AN: 67712

Other (OTH) AF: 0.200 AC: 420 AN: 2104

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10920501; hg19: chr1-190061945;