6-159570636-T-C

Variant names:

• chr6-159570636-T-C
• rs12192410
• ENST00000656085.1:n.42+91950A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656085.1(ENSG00000286533):​n.42+91950A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,096 control chromosomes in the GnomAD database, including 2,305 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 0.17 (2305 hom., cov: 32)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 2 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656085.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286533	ENST00000656085.1		n.42+91950A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25292 AN: 151978 Hom.: 2302 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.166 AC: 25311 AN: 152096 Hom.: 2305 Cov.: 32 AF XY: 0.167 AC XY: 12446 AN XY: 74360

African (AFR) AF: 0.250 AC: 10343 AN: 41432

American (AMR) AF: 0.130 AC: 1985 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3472

East Asian (EAS) AF: 0.175 AC: 906 AN: 5166

South Asian (SAS) AF: 0.202 AC: 976 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10588

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8863 AN: 67994

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.152 Hom.: 326

Bravo AF: 0.166

Asia WGS AF: 0.187 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.37
PhyloP100		-0.058

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12192410;

hg19: chr6-159991668;