rs510153

Variant names:

• chr6-33602298-G-A
• rs510153

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.264

Alfa AF: 0.255 Hom.: 2253

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs510153; hg19: chr6-33570075;