1-115134562-T-C

Variant names:

• chr1-115134562-T-C
• rs2078371

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 0.14 in 151,990 control chromosomes in the GnomAD database, including 1,613 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 0.14 (1613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21319 AN: 151872 Hom.: 1607 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.140 AC: 21351 AN: 151990 Hom.: 1613 Cov.: 32 AF XY: 0.142 AC XY: 10545 AN XY: 74292

African (AFR) AF: 0.204 AC: 8455 AN: 41436

American (AMR) AF: 0.118 AC: 1797 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.0776 AC: 400 AN: 5154

South Asian (SAS) AF: 0.104 AC: 498 AN: 4806

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10572

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7905 AN: 67960

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.121 Hom.: 1990

Bravo AF: 0.140

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.30
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs2078371; hg19: chr1-115677183;