chr6-31272915-G-A

Variant names:

• chr6-31272915-G-A
• rs2395471
• ENST00000755297.1:n.32+1809G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+1809G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,966 control chromosomes in the GnomAD database, including 17,211 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 0.47 (17211 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 45 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+1809G>A		intron	N/A
	ENSG00000288813	ENST00000692808.2		n.*46G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71331 AN: 151848 Hom.: 17191 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.470 AC: 71398 AN: 151966 Hom.: 17211 Cov.: 31 AF XY: 0.477 AC XY: 35417 AN XY: 74278

African (AFR) AF: 0.536 AC: 22206 AN: 41448

American (AMR) AF: 0.493 AC: 7535 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2301 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2382 AN: 5176

South Asian (SAS) AF: 0.616 AC: 2969 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4772 AN: 10534

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27500 AN: 67936

Other (OTH) AF: 0.530 AC: 1117 AN: 2108

Alfa AF: 0.423 Hom.: 35319

Bravo AF: 0.474

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.4
DANN	Benign	0.32
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs2395471; hg19: chr6-31240692;