rs2842992

Positions:

• chr6-159650127-G-A

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, non coding transcript 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: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656085.1	n.42+12459C>T		intron_variant, non_coding_transcript_variant

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;