rs6867736

Variant names:

• chr5-38250903-G-A
• rs6867736

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 0.248 in 151,812 control chromosomes in the GnomAD database, including 5,394 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 0.25 (5394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 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: 0.248 AC: 37646 AN: 151694 Hom.: 5401 Cov.: 31

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.248 AC: 37632 AN: 151812 Hom.: 5394 Cov.: 31 AF XY: 0.246 AC XY: 18284 AN XY: 74180

African (AFR) AF: 0.112 AC: 4633 AN: 41420

American (AMR) AF: 0.271 AC: 4138 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3468

East Asian (EAS) AF: 0.144 AC: 740 AN: 5140

South Asian (SAS) AF: 0.183 AC: 878 AN: 4796

European-Finnish (FIN) AF: 0.305 AC: 3208 AN: 10516

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22075 AN: 67922

Other (OTH) AF: 0.266 AC: 559 AN: 2098

Alfa AF: 0.299 Hom.: 12410

Bravo AF: 0.243

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.42
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs6867736; hg19: chr5-38251005;