chr5-123195653-G-A

Variant names:

• chr5-123195653-G-A
• rs17470137

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 0.194 in 152,132 control chromosomes in the GnomAD database, including 3,689 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 0.19 (3689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 20 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 (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.194 AC: 29542 AN: 152014 Hom.: 3688 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.194 AC: 29542 AN: 152132 Hom.: 3689 Cov.: 32 AF XY: 0.193 AC XY: 14352 AN XY: 74350

African (AFR) AF: 0.0610 AC: 2533 AN: 41534

American (AMR) AF: 0.184 AC: 2818 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3468

East Asian (EAS) AF: 0.00618 AC: 32 AN: 5174

South Asian (SAS) AF: 0.116 AC: 559 AN: 4814

European-Finnish (FIN) AF: 0.322 AC: 3401 AN: 10568

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18420 AN: 67976

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.237 Hom.: 14870

Bravo AF: 0.180

Asia WGS AF: 0.0610 AC: 217 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	1.1
DANN	Benign	0.73
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs17470137; hg19: chr5-122531347;