10-93489848-A-G

Variant names:

• chr10-93489848-A-G
• rs947603

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 0.267 in 152,024 control chromosomes in the GnomAD database, including 6,084 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 0.27 (6084 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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: 0.267 AC: 40549 AN: 151906 Hom.: 6083 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.267 AC: 40563 AN: 152024 Hom.: 6084 Cov.: 31 AF XY: 0.272 AC XY: 20243 AN XY: 74322

African (AFR) AF: 0.235 AC: 9753 AN: 41458

American (AMR) AF: 0.284 AC: 4333 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3470

East Asian (EAS) AF: 0.748 AC: 3858 AN: 5158

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2941 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16031 AN: 67954

Other (OTH) AF: 0.294 AC: 621 AN: 2112

Alfa AF: 0.256 Hom.: 24060

Bravo AF: 0.273

Asia WGS AF: 0.459 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs947603; hg19: chr10-95249605;