6-139514552-C-T

Position:

• chr6-139514552-C-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, non coding transcript 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: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647815.1	n.134+27937C>T		intron_variant, non_coding_transcript_variant

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;