ENST00000656085.1:n.43-52408C>T

Variant names:

• chr6-159521923-G-A
• rs12197995
• ENST00000656085.1:n.43-52408C>T

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.43-52408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,022 control chromosomes in the GnomAD database, including 6,811 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 0.27 (6811 hom., cov: 31)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 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.43-52408C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41321 AN: 151902 Hom.: 6814 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.0280

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.272 AC: 41316 AN: 152022 Hom.: 6811 Cov.: 31 AF XY: 0.268 AC XY: 19942 AN XY: 74322

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.0281

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.289

Alfa AF: 0.346 Hom.: 7890

Bravo AF: 0.257

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12197995; hg19: chr6-159942955; COSMIC: COSV68549806;