rs3094159

Positions:

• chr6-29868057-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1	n.2063-10619C>T		intron_variant

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

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.619

Alfa AF: 0.642 Hom.: 16742

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094159; hg19: chr6-29835834;