chr6-139514552-C-T

Variant names:

• chr6-139514552-C-T
• rs668459
• ENST00000647815.1:n.134+27937C>T

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+27937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,930 control chromosomes in the GnomAD database, including 20,726 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 (20726 hom., cov: 31)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 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+27937C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77509 AN: 151812 Hom.: 20706 Cov.: 31

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.510 AC: 77557 AN: 151930 Hom.: 20726 Cov.: 31 AF XY: 0.511 AC XY: 37932 AN XY: 74244

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.535

Alfa AF: 0.582 Hom.: 56560

Bravo AF: 0.503

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.92
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs668459; hg19: chr6-139835689;