6-31379160-G-A

Variant names:

• chr6-31379160-G-A
• rs9501587
• ENST00000755446.1:n.327-2820G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755446.1(ENSG00000298426):​n.327-2820G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 20 publications found

Genes affected

ENSG00000298426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-2820G>A		intron	N/A

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

African (AFR) AF: 0.451 AC: 18682 AN: 41398

American (AMR) AF: 0.342 AC: 5230 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3472

East Asian (EAS) AF: 0.144 AC: 742 AN: 5162

South Asian (SAS) AF: 0.322 AC: 1549 AN: 4810

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10576

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13584 AN: 67998

Other (OTH) AF: 0.331 AC: 698 AN: 2108

Alfa AF: 0.216 Hom.: 12706

Bravo AF: 0.308

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.89
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9501587; hg19: chr6-31346937;