6-31370608-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649421.1(ENSG00000285647):n.274+3278T>C variant causes a intron, non coding transcript 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: ENST00000649421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649421.1	n.274+3278T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.594

Alfa AF: 0.586 Hom.: 4530

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9266455; hg19: chr6-31338385;