rs10484515

Variant names:

• chr6-163974368-C-A
• rs10484515
• ENST00000659063.1:n.43-34156C>A

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-34156C>A 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 151,924 control chromosomes in the GnomAD database, including 5,442 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 (5442 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000659063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 2 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 = 0.34 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.43-34156C>A		intron	N/A
	ENSG00000288696	ENST00000850151.1		n.105+47322C>A		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.165+47322C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39607 AN: 151802 Hom.: 5432 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.261 AC: 39648 AN: 151924 Hom.: 5442 Cov.: 32 AF XY: 0.257 AC XY: 19061 AN XY: 74266

African (AFR) AF: 0.345 AC: 14286 AN: 41410

American (AMR) AF: 0.292 AC: 4454 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5164

South Asian (SAS) AF: 0.164 AC: 792 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1867 AN: 10566

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15708 AN: 67908

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.249 Hom.: 610

Bravo AF: 0.277

Asia WGS AF: 0.183 AC: 637 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		0.13

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: rs10484515;

hg19: chr6-164395400;