rs10484514

chr6-163975756-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659063.1(ENSG00000288696):n.43-32768C>T variant causes a intron, non coding transcript 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: ENST00000659063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378102	XR_943213.4	n.558+55842C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659063.1	n.43-32768C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.202

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.7
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484514; hg19: chr6-164396788;