rs9501587

Positions:

• chr6-31379160-G-A
• chr6-31379160-G-C

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 0.288 in 152,000 control chromosomes in the GnomAD database, including 7,297 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 0.29 (7297 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31379160G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43735 AN: 151884 Hom.: 7290 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.288 AC: 43786 AN: 152000 Hom.: 7297 Cov.: 31 AF XY: 0.289 AC XY: 21447 AN XY: 74306

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.331

Alfa AF: 0.206 Hom.: 3069

Bravo AF: 0.308

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9501587; hg19: chr6-31346937;