rs3094157

Variant names:

• chr6-29868462-C-G
• rs3094157
• ENST00000647952.1:n.2063-11024G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-29868462-C-G
• chr6-29868462-C-T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-11024G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,278 control chromosomes in the GnomAD database, including 58,848 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 0.88 (58848 hom., cov: 33)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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.2063-11024G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133403 AN: 152160 Hom.: 58785 Cov.: 33

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.877 AC: 133525 AN: 152278 Hom.: 58848 Cov.: 33 AF XY: 0.873 AC XY: 65008 AN XY: 74460

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.893

Alfa AF: 0.863 Hom.: 7047

Bravo AF: 0.894

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.63
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094157; hg19: chr6-29836239;