6-139514552-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 34 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647815.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226571	ENST00000647815.1		n.134+27937C>T		intron	N/A
	ENSG00000226571	ENST00000775574.1		n.194-32690C>T		intron	N/A

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

African (AFR) AF: 0.358 AC: 14846 AN: 41428

American (AMR) AF: 0.559 AC: 8534 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2230 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1585 AN: 5160

South Asian (SAS) AF: 0.701 AC: 3369 AN: 4808

European-Finnish (FIN) AF: 0.492 AC: 5180 AN: 10528

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39983 AN: 67956

Other (OTH) AF: 0.535 AC: 1127 AN: 2106

Alfa AF: 0.566 Hom.: 112382

Bravo AF: 0.503

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.92
DANN	Benign	0.67
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs668459;

hg19: chr6-139835689;