rs510153

Variant names:

• chr6-33602298-G-A
• rs510153
• ENST00000838175.1:n.201-87C>T

Variant summary

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

The ENST00000838175.1(ENSG00000309063):​n.201-87C>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 151,928 control chromosomes in the GnomAD database, including 5,570 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 (5570 hom., cov: 32)
• Consequence: ENSG00000309063 ENST00000838175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 publications found

Genes affected

ENSG00000309063 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309063	ENST00000838175.1	n.201-87C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39543 AN: 151810 Hom.: 5567 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.261 AC: 39582 AN: 151928 Hom.: 5570 Cov.: 32 AF XY: 0.272 AC XY: 20174 AN XY: 74226

African (AFR) AF: 0.214 AC: 8890 AN: 41474

American (AMR) AF: 0.340 AC: 5185 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3466

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5166

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4818

European-Finnish (FIN) AF: 0.355 AC: 3751 AN: 10556

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15778 AN: 67914

Other (OTH) AF: 0.264 AC: 556 AN: 2104

Alfa AF: 0.252 Hom.: 2470

Bravo AF: 0.257

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs510153; hg19: chr6-33570075;