ENST00000649421.2:n.648A>T

Variant names:

• chr6-31375256-A-T
• rs2507987
• ENST00000649421.2:n.648A>T

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.648A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,972 control chromosomes in the GnomAD database, including 23,801 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 0.55 (23801 hom., cov: 31)
• Consequence: ENSG00000285647 ENST00000649421.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 15 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 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
ENSG00000285647	ENST00000649421.2	n.648A>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285647	ENST00000755530.1	n.576A>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298426	ENST00000755446.1	n.327-6724A>T		intron_variant	Intron 1 of 1
ENSG00000298474	ENST00000755731.1	n.*80T>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84287 AN: 151856 Hom.: 23785 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.555 AC: 84338 AN: 151972 Hom.: 23801 Cov.: 31 AF XY: 0.551 AC XY: 40892 AN XY: 74266

African (AFR) AF: 0.495 AC: 20499 AN: 41400

American (AMR) AF: 0.480 AC: 7335 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3495 AN: 5166

South Asian (SAS) AF: 0.593 AC: 2859 AN: 4822

European-Finnish (FIN) AF: 0.498 AC: 5240 AN: 10532

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.612 AC: 41568 AN: 67976

Other (OTH) AF: 0.578 AC: 1219 AN: 2110

Alfa AF: 0.460 Hom.: 1334

Bravo AF: 0.550

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2507987; hg19: chr6-31343033;