rs2842992

Variant names:

• chr6-159650127-G-A
• rs2842992
• ENST00000656085.1:n.42+12459C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-159650127-G-A
• chr6-159650127-G-C
• chr6-159650127-G-T

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+12459C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,194 control chromosomes in the GnomAD database, including 41,083 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 0.73 (41083 hom., cov: 34)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.802 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
ENSG00000286533	ENST00000656085.1	n.42+12459C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110557 AN: 152076 Hom.: 41070 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.727 AC: 110608 AN: 152194 Hom.: 41083 Cov.: 34 AF XY: 0.730 AC XY: 54302 AN XY: 74408

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.737

Alfa AF: 0.769 Hom.: 52644

Bravo AF: 0.716

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2842992; hg19: chr6-160071159;