rs6867736

Variant names:

• chr5-38250903-G-A
• rs6867736

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.266

Alfa AF: 0.304 Hom.: 10086

Bravo AF: 0.243

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6867736; hg19: chr5-38251005;