rs12136856

chr1-156503322-C-G

Variant summary

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

The ENST00000689293.1(ENSG00000288835):n.240C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,848 control chromosomes in the GnomAD database, including 25,042 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 0.55 (25042 hom., cov: 30)
• Consequence: ENST00000689293.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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
	ENST00000689293.1	n.240C>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83842 AN: 151730 Hom.: 25032 Cov.: 30

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.552 AC: 83870 AN: 151848 Hom.: 25042 Cov.: 30 AF XY: 0.553 AC XY: 41065 AN XY: 74208

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.618

Alfa AF: 0.485 Hom.: 1579

Bravo AF: 0.541

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	9.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12136856; hg19: chr1-156473114;