rs3115619

Variant names:

• chr6-29875102-A-G
• rs3115619
• ENST00000647952.1:n.2062+8452T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-29875102-A-G
• chr6-29875102-A-T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2062+8452T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 150,596 control chromosomes in the GnomAD database, including 29,027 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 0.62 (29027 hom., cov: 27)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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

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
	ENSG00000290870	ENST00000647952.1		n.2062+8452T>C		intron	N/A
	POLR1HASP	ENST00000849679.1		n.586+11184T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 93290 AN: 150482 Hom.: 28992 Cov.: 27

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.620 AC: 93372 AN: 150596 Hom.: 29027 Cov.: 27 AF XY: 0.613 AC XY: 45053 AN XY: 73534

African (AFR) AF: 0.626 AC: 25542 AN: 40778

American (AMR) AF: 0.614 AC: 9267 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2274 AN: 3450

East Asian (EAS) AF: 0.460 AC: 2350 AN: 5112

South Asian (SAS) AF: 0.522 AC: 2460 AN: 4716

European-Finnish (FIN) AF: 0.543 AC: 5670 AN: 10434

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.646 AC: 43775 AN: 67734

Other (OTH) AF: 0.615 AC: 1279 AN: 2080

Alfa AF: 0.628 Hom.: 11263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.7
DANN	Benign	0.44
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs3115619; hg19: chr6-29842879;