6-31344761-G-A

Variant names:

• chr6-31344761-G-A
• rs2854008
• ENST00000755297.1:n.33-11440G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-11440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,870 control chromosomes in the GnomAD database, including 3,504 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 0.20 (3504 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 14 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 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
ENSG00000298396	ENST00000755297.1	n.33-11440G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30797 AN: 151756 Hom.: 3506 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.203 AC: 30802 AN: 151870 Hom.: 3504 Cov.: 32 AF XY: 0.194 AC XY: 14402 AN XY: 74252

African (AFR) AF: 0.145 AC: 5990 AN: 41436

American (AMR) AF: 0.169 AC: 2576 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 708 AN: 3462

East Asian (EAS) AF: 0.208 AC: 1070 AN: 5156

South Asian (SAS) AF: 0.172 AC: 828 AN: 4804

European-Finnish (FIN) AF: 0.147 AC: 1554 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17354 AN: 67878

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.224 Hom.: 2171

Bravo AF: 0.203

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2854008; hg19: chr6-31312538;