chr5-170827611-G-A

Variant names:

• chr5-170827611-G-A
• rs752596

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 0.43 in 151,154 control chromosomes in the GnomAD database, including 15,762 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 0.43 (15762 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.430 AC: 64987 AN: 151034 Hom.: 15754 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.430 AC: 64997 AN: 151154 Hom.: 15762 Cov.: 31 AF XY: 0.436 AC XY: 32212 AN XY: 73876

African (AFR) AF: 0.206 AC: 8383 AN: 40688

American (AMR) AF: 0.534 AC: 8147 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1844 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3665 AN: 5140

South Asian (SAS) AF: 0.671 AC: 3234 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4646 AN: 10530

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33289 AN: 67944

Other (OTH) AF: 0.476 AC: 999 AN: 2100

Alfa AF: 0.484 Hom.: 12097

Bravo AF: 0.423

Asia WGS AF: 0.634 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.90
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs752596; hg19: chr5-170254615; COSMIC: COSV60230384;