6-139486909-C-T

Variant names:

• chr6-139486909-C-T
• rs1468708
• ENST00000647815.1:n.134+294C>T

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,074 control chromosomes in the GnomAD database, including 35,005 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 0.67 (35005 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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
ENSG00000226571	ENST00000647815.1	n.134+294C>T		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000647987.1	n.204+294C>T		intron_variant	Intron 1 of 1
ENSG00000226571	ENST00000650173.1	n.1279-19555C>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101915 AN: 151956 Hom.: 34967 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.671 AC: 102008 AN: 152074 Hom.: 35005 Cov.: 32 AF XY: 0.670 AC XY: 49814 AN XY: 74310

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.640

Alfa AF: 0.610 Hom.: 13818

Bravo AF: 0.675

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468708; hg19: chr6-139808046; COSMIC: COSV60286761;