10-53447468-C-G

Variant names:

• chr10-53447468-C-G
• rs10740548

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 0.497 in 152,094 control chromosomes in the GnomAD database, including 19,260 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 0.50 (19260 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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: 0.497 AC: 75597 AN: 151976 Hom.: 19256 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.497 AC: 75635 AN: 152094 Hom.: 19260 Cov.: 33 AF XY: 0.504 AC XY: 37512 AN XY: 74364

African (AFR) AF: 0.464 AC: 19236 AN: 41496

American (AMR) AF: 0.505 AC: 7712 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4233 AN: 5166

South Asian (SAS) AF: 0.579 AC: 2790 AN: 4820

European-Finnish (FIN) AF: 0.511 AC: 5395 AN: 10566

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32457 AN: 67986

Other (OTH) AF: 0.525 AC: 1107 AN: 2108

Alfa AF: 0.328 Hom.: 794

Bravo AF: 0.496

Asia WGS AF: 0.657 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10740548; hg19: chr10-55207228;