rs10484702

Positions:

• chr6-145206921-T-C

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 0.474 in 151,948 control chromosomes in the GnomAD database, including 18,095 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 0.47 (18095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71972 AN: 151830 Hom.: 18092 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.474 AC: 71996 AN: 151948 Hom.: 18095 Cov.: 32 AF XY: 0.478 AC XY: 35469 AN XY: 74248

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.527

Alfa AF: 0.523 Hom.: 43000

Bravo AF: 0.482

Asia WGS AF: 0.546 AC: 1896 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484702; hg19: chr6-145528057;