rs10484324

Variant names:

• chr6-7515112-C-A
• rs10484324

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 0.0347 in 152,322 control chromosomes in the GnomAD database, including 203 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 0.035 (203 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0886 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: 0.0346 AC: 5272 AN: 152204 Hom.: 202 Cov.: 33

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.00910

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00905

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0347 AC: 5281 AN: 152322 Hom.: 203 Cov.: 33 AF XY: 0.0340 AC XY: 2529 AN XY: 74482

African (AFR) AF: 0.0910 AC: 3783 AN: 41558

American (AMR) AF: 0.0260 AC: 398 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3468

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5190

South Asian (SAS) AF: 0.00911 AC: 44 AN: 4830

European-Finnish (FIN) AF: 0.0104 AC: 110 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00904 AC: 615 AN: 68038

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

Alfa AF: 0.0178 Hom.: 118

Bravo AF: 0.0398

Asia WGS AF: 0.0240 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.80
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10484324; hg19: chr6-7515345;