rs10484702

Variant names:

• chr6-145206921-T-C
• rs10484702

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.305 AC: 12637 AN: 41454

American (AMR) AF: 0.631 AC: 9627 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2066 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3245 AN: 5148

South Asian (SAS) AF: 0.613 AC: 2953 AN: 4818

European-Finnish (FIN) AF: 0.438 AC: 4606 AN: 10526

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 34991 AN: 67958

Other (OTH) AF: 0.527 AC: 1110 AN: 2106

Alfa AF: 0.511 Hom.: 85713

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
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs10484702; hg19: chr6-145528057;