6-159647936-G-A

Variant names:

• chr6-159647936-G-A
• rs911847
• ENST00000656085.1:n.42+14650C>T

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+14650C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,948 control chromosomes in the GnomAD database, including 7,638 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 0.31 (7638 hom., cov: 31)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 12 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286533	ENST00000656085.1		n.42+14650C>T		intron	N/A
	ENSG00000286533	ENST00000794978.1		n.185+14547C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47062 AN: 151830 Hom.: 7626 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.310 AC: 47089 AN: 151948 Hom.: 7638 Cov.: 31 AF XY: 0.305 AC XY: 22657 AN XY: 74248

African (AFR) AF: 0.382 AC: 15834 AN: 41432

American (AMR) AF: 0.322 AC: 4919 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 921 AN: 3468

East Asian (EAS) AF: 0.163 AC: 844 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1527 AN: 4806

European-Finnish (FIN) AF: 0.215 AC: 2272 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19713 AN: 67930

Other (OTH) AF: 0.307 AC: 647 AN: 2106

Alfa AF: 0.295 Hom.: 13950

Bravo AF: 0.319

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.28
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs911847; hg19: chr6-160068968;