6-31452241-T-C

Variant names:

• chr6-31452241-T-C
• rs2516456
• ENST00000673857.1:n.63-10882T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-10882T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,592 control chromosomes in the GnomAD database, including 20,571 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 0.51 (20571 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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.63-10882T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77420 AN: 151474 Hom.: 20537 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.511 AC: 77493 AN: 151592 Hom.: 20571 Cov.: 31 AF XY: 0.506 AC XY: 37494 AN XY: 74100

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.517

Alfa AF: 0.502 Hom.: 12906

Bravo AF: 0.518

Asia WGS AF: 0.343 AC: 1191 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516456; hg19: chr6-31420018;