ENST00000647952.1:n.2063-4267T>G

Variant names:

• chr6-29861705-A-C
• rs1611715
• ENST00000647952.1:n.2063-4267T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647952.1(ENSG00000290870):​n.2063-4267T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,146 control chromosomes in the GnomAD database, including 6,925 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 0.30 (6925 hom., cov: 32)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 19 publications found

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647952.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290870	ENST00000647952.1		n.2063-4267T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45302 AN: 152028 Hom.: 6919 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.298 AC: 45326 AN: 152146 Hom.: 6925 Cov.: 32 AF XY: 0.295 AC XY: 21972 AN XY: 74376

African (AFR) AF: 0.241 AC: 10011 AN: 41488

American (AMR) AF: 0.306 AC: 4679 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1888 AN: 5192

South Asian (SAS) AF: 0.165 AC: 798 AN: 4824

European-Finnish (FIN) AF: 0.345 AC: 3644 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22543 AN: 67988

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.316 Hom.: 14074

Bravo AF: 0.297

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1611715; hg19: chr6-29829482;