5-99952242-T-C

Variant names:

• chr5-99952242-T-C
• rs10515289

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 0.229 in 152,046 control chromosomes in the GnomAD database, including 4,221 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 0.23 (4221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 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: 0.229 AC: 34851 AN: 151928 Hom.: 4217 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0480

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.229 AC: 34874 AN: 152046 Hom.: 4221 Cov.: 32 AF XY: 0.226 AC XY: 16800 AN XY: 74346

African (AFR) AF: 0.200 AC: 8287 AN: 41472

American (AMR) AF: 0.230 AC: 3507 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3464

East Asian (EAS) AF: 0.0479 AC: 248 AN: 5178

South Asian (SAS) AF: 0.0880 AC: 424 AN: 4820

European-Finnish (FIN) AF: 0.272 AC: 2869 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17641 AN: 67968

Other (OTH) AF: 0.256 AC: 540 AN: 2110

Alfa AF: 0.250 Hom.: 15564

Bravo AF: 0.228

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.50
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10515289; hg19: chr5-99287946;