rs2254386

Variant names:

• chr6-31457256-T-C
• rs2254386
• ENST00000673857.1:n.63-5867T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-5867T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,608 control chromosomes in the GnomAD database, including 22,127 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 0.53 (22127 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 11 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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
ENSG00000288587	ENST00000673857.1	n.63-5867T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80568 AN: 151490 Hom.: 22083 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.532 AC: 80660 AN: 151608 Hom.: 22127 Cov.: 31 AF XY: 0.527 AC XY: 39067 AN XY: 74100

African (AFR) AF: 0.576 AC: 23720 AN: 41214

American (AMR) AF: 0.560 AC: 8493 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2023 AN: 3464

East Asian (EAS) AF: 0.293 AC: 1507 AN: 5150

South Asian (SAS) AF: 0.465 AC: 2242 AN: 4824

European-Finnish (FIN) AF: 0.516 AC: 5442 AN: 10554

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.521 AC: 35361 AN: 67932

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.528 Hom.: 22829

Bravo AF: 0.537

Asia WGS AF: 0.391 AC: 1360 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.34
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2254386; hg19: chr6-31425033;