6-88036373-G-C

Variant names:

• chr6-88036373-G-C
• rs269423

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 0.239 in 152,080 control chromosomes in the GnomAD database, including 5,469 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 0.24 (5469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.239 AC: 36342 AN: 151960 Hom.: 5467 Cov.: 32

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.239 AC: 36344 AN: 152080 Hom.: 5469 Cov.: 32 AF XY: 0.245 AC XY: 18176 AN XY: 74336

African (AFR) AF: 0.0586 AC: 2433 AN: 41510

American (AMR) AF: 0.326 AC: 4971 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3464

East Asian (EAS) AF: 0.462 AC: 2386 AN: 5168

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4820

European-Finnish (FIN) AF: 0.388 AC: 4094 AN: 10562

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19744 AN: 67980

Other (OTH) AF: 0.224 AC: 474 AN: 2112

Alfa AF: 0.152 Hom.: 330

Bravo AF: 0.228

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.3
DANN	Benign	0.75
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs269423; hg19: chr6-88746091;