rs1992662

Variant names:

• chr5-40393750-A-G
• rs1992662

Your query was ambiguous. Multiple possible variants found:

• chr5-40393750-A-G
• chr5-40393750-A-T

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 0.303 in 151,922 control chromosomes in the GnomAD database, including 7,830 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 0.30 (7830 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46013 AN: 151802 Hom.: 7831 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 46026 AN: 151922 Hom.: 7830 Cov.: 31 AF XY: 0.311 AC XY: 23054 AN XY: 74224

African (AFR) AF: 0.191 AC: 7920 AN: 41482

American (AMR) AF: 0.310 AC: 4715 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3786 AN: 5148

South Asian (SAS) AF: 0.453 AC: 2184 AN: 4816

European-Finnish (FIN) AF: 0.391 AC: 4127 AN: 10560

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21388 AN: 67902

Other (OTH) AF: 0.303 AC: 640 AN: 2110

Alfa AF: 0.298 Hom.: 2692

Bravo AF: 0.290

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1992662; hg19: chr5-40393852;