1-115630459-G-T

Variant names:

• chr1-115630459-G-T
• rs7523839

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 0.597 in 152,090 control chromosomes in the GnomAD database, including 31,358 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 0.60 (31358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90759 AN: 151972 Hom.: 31363 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.597 AC: 90774 AN: 152090 Hom.: 31358 Cov.: 32 AF XY: 0.597 AC XY: 44396 AN XY: 74356

African (AFR) AF: 0.221 AC: 9151 AN: 41452

American (AMR) AF: 0.709 AC: 10822 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3866 AN: 5180

South Asian (SAS) AF: 0.597 AC: 2878 AN: 4822

European-Finnish (FIN) AF: 0.701 AC: 7419 AN: 10582

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51521 AN: 67990

Other (OTH) AF: 0.658 AC: 1393 AN: 2116

Alfa AF: 0.660 Hom.: 6080

Bravo AF: 0.586

Asia WGS AF: 0.617 AC: 2148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.4
DANN	Benign	0.90
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7523839; hg19: chr1-116173080;