6-29868057-G-A

Variant names:

• chr6-29868057-G-A
• rs3094159
• ENST00000647952.1:n.2063-10619C>T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-10619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,882 control chromosomes in the GnomAD database, including 29,584 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 0.62 (29584 hom., cov: 31)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 22 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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.2063-10619C>T		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1	n.587-5231C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94467 AN: 151764 Hom.: 29547 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.623 AC: 94553 AN: 151882 Hom.: 29584 Cov.: 31 AF XY: 0.615 AC XY: 45681 AN XY: 74222

African (AFR) AF: 0.631 AC: 26128 AN: 41392

American (AMR) AF: 0.617 AC: 9424 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3468

East Asian (EAS) AF: 0.465 AC: 2395 AN: 5154

South Asian (SAS) AF: 0.527 AC: 2533 AN: 4806

European-Finnish (FIN) AF: 0.546 AC: 5739 AN: 10516

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43979 AN: 67966

Other (OTH) AF: 0.619 AC: 1305 AN: 2108

Alfa AF: 0.635 Hom.: 26996

Bravo AF: 0.631

Asia WGS AF: 0.458 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.20
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs3094159; hg19: chr6-29835834;