6-164005733-A-G

Variant names:

• chr6-164005733-A-G
• rs206003
• ENST00000659063.1:n.43-2791A>G

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-2791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,142 control chromosomes in the GnomAD database, including 50,099 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 0.81 (50099 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000659063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 4 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659063.1. 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
	ENSG00000288696	ENST00000659063.1		n.43-2791A>G		intron	N/A
	ENSG00000288696	ENST00000850151.1		n.106-51315A>G		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.166-51315A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123182 AN: 152024 Hom.: 50029 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.811 AC: 123317 AN: 152142 Hom.: 50099 Cov.: 32 AF XY: 0.814 AC XY: 60512 AN XY: 74368

African (AFR) AF: 0.864 AC: 35854 AN: 41496

American (AMR) AF: 0.825 AC: 12617 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2827 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4257 AN: 5158

South Asian (SAS) AF: 0.825 AC: 3980 AN: 4822

European-Finnish (FIN) AF: 0.822 AC: 8708 AN: 10594

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52348 AN: 67990

Other (OTH) AF: 0.802 AC: 1690 AN: 2108

Alfa AF: 0.783 Hom.: 57999

Bravo AF: 0.817

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.57
PhyloP100		-1.1

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: rs206003;

hg19: chr6-164426765;