6-163975756-C-T

Variant names:

• chr6-163975756-C-T
• rs10484514
• ENST00000659063.1:n.43-32768C>T

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-32768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,098 control chromosomes in the GnomAD database, including 2,894 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 0.19 (2894 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000659063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 3 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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.43-32768C>T		intron	N/A
	ENSG00000288696	ENST00000850151.1		n.105+48710C>T		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.165+48710C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29137 AN: 151980 Hom.: 2896 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.192 AC: 29135 AN: 152098 Hom.: 2894 Cov.: 32 AF XY: 0.190 AC XY: 14092 AN XY: 74344

African (AFR) AF: 0.137 AC: 5682 AN: 41510

American (AMR) AF: 0.181 AC: 2760 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5174

South Asian (SAS) AF: 0.166 AC: 800 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15640 AN: 67982

Other (OTH) AF: 0.202 AC: 425 AN: 2104

Alfa AF: 0.200 Hom.: 481

Bravo AF: 0.188

Asia WGS AF: 0.151 AC: 525 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	2.7
DANN	Benign	0.36
PhyloP100		-0.062

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: rs10484514;

hg19: chr6-164396788;