rs12197995

chr6-159521923-G-A

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, non coding transcript 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: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656085.1	n.43-52408C>T		intron_variant, non_coding_transcript_variant

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;