ENST00000649421.2:n.274+3278T>C

Variant names:

• chr6-31370608-T-C
• rs9266455
• ENST00000649421.2:n.274+3278T>C

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.274+3278T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 150,482 control chromosomes in the GnomAD database, including 25,524 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 0.57 (25524 hom., cov: 31)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 7 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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.274+3278T>C		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-11372T>C		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-4275T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 85800 AN: 150368 Hom.: 25503 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.606

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.571 AC: 85859 AN: 150482 Hom.: 25524 Cov.: 31 AF XY: 0.568 AC XY: 41654 AN XY: 73336

African (AFR) AF: 0.500 AC: 20641 AN: 41292

American (AMR) AF: 0.529 AC: 7830 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3460

East Asian (EAS) AF: 0.735 AC: 3692 AN: 5020

South Asian (SAS) AF: 0.663 AC: 3051 AN: 4604

European-Finnish (FIN) AF: 0.512 AC: 5293 AN: 10328

Middle Eastern (MID) AF: 0.601 AC: 173 AN: 288

European-Non Finnish (NFE) AF: 0.620 AC: 41955 AN: 67682

Other (OTH) AF: 0.594 AC: 1243 AN: 2092

Alfa AF: 0.585 Hom.: 5001

Bravo AF: 0.569

Asia WGS AF: 0.661 AC: 2252 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.6
DANN	Benign	0.13
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9266455; hg19: chr6-31338385;