ENST00000647952.1:n.2063-3701G>A

Variant names:

• chr6-29861139-C-T
• rs1611710
• ENST00000647952.1:n.2063-3701G>A

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-3701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,906 control chromosomes in the GnomAD database, including 15,584 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 0.45 (15584 hom., cov: 30)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 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
ENSG00000290870	ENST00000647952.1	n.2063-3701G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68412 AN: 151788 Hom.: 15565 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.451 AC: 68459 AN: 151906 Hom.: 15584 Cov.: 30 AF XY: 0.448 AC XY: 33276 AN XY: 74244

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.475

Alfa AF: 0.437 Hom.: 5748

Bravo AF: 0.463

Asia WGS AF: 0.579 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611710; hg19: chr6-29828916;