6-159529503-A-G

Variant names:

• chr6-159529503-A-G
• rs382440
• ENST00000656085.1:n.43-59988T>C

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.43-59988T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,084 control chromosomes in the GnomAD database, including 12,049 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 0.38 (12049 hom., cov: 33)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• 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 (EAS) allele frequency at 95% confidence interval = 0.765 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.43-59988T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57254 AN: 151966 Hom.: 12019 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.377 AC: 57335 AN: 152084 Hom.: 12049 Cov.: 33 AF XY: 0.385 AC XY: 28584 AN XY: 74314

African (AFR) AF: 0.504 AC: 20873 AN: 41448

American (AMR) AF: 0.401 AC: 6137 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3470

East Asian (EAS) AF: 0.785 AC: 4067 AN: 5178

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3600 AN: 10568

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18044 AN: 67998

Other (OTH) AF: 0.389 AC: 822 AN: 2112

Alfa AF: 0.300 Hom.: 1527

Bravo AF: 0.390

Asia WGS AF: 0.632 AC: 2194 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	1.3
DANN	Benign	0.69
PhyloP100		-0.95

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: rs382440;

hg19: chr6-159950535;