ENST00000647815.1:n.134+21914C>T

Variant names:

• chr6-139508529-C-T
• rs605066
• ENST00000647815.1:n.134+21914C>T

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+21914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,802 control chromosomes in the GnomAD database, including 22,164 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 0.53 (22164 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 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+21914C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81039 AN: 151684 Hom.: 22142 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.534 AC: 81091 AN: 151802 Hom.: 22164 Cov.: 32 AF XY: 0.533 AC XY: 39542 AN XY: 74162

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.556

Alfa AF: 0.563 Hom.: 13816

Bravo AF: 0.529

Asia WGS AF: 0.514 AC: 1787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.47
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs605066; hg19: chr6-139829666;