6-163978423-C-T

Variant names:

• chr6-163978423-C-T
• rs10484512
• ENST00000659063.1:n.43-30101C>T

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-30101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,036 control chromosomes in the GnomAD database, including 5,440 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 0.26 (5440 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000659063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378102	XR_943213.4	n.558+58509C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288696	ENST00000659063.1	n.43-30101C>T		intron_variant	Intron 1 of 1
ENSG00000288696	ENST00000850151.1	n.105+51377C>T		intron_variant	Intron 1 of 4
ENSG00000288696	ENST00000850152.1	n.165+51377C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39654 AN: 151916 Hom.: 5430 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.261 AC: 39696 AN: 152036 Hom.: 5440 Cov.: 32 AF XY: 0.257 AC XY: 19073 AN XY: 74318

African (AFR) AF: 0.343 AC: 14233 AN: 41450

American (AMR) AF: 0.293 AC: 4470 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1114 AN: 5156

South Asian (SAS) AF: 0.165 AC: 798 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1865 AN: 10550

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15776 AN: 67986

Other (OTH) AF: 0.256 AC: 542 AN: 2116

Alfa AF: 0.238 Hom.: 556

Bravo AF: 0.276

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.42
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10484512; hg19: chr6-164399455;