rs10052004

Variant names:

• chr5-57370673-G-A
• rs10052004

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 0.251 in 151,898 control chromosomes in the GnomAD database, including 5,467 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 0.25 (5467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 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: 0.251 AC: 38081 AN: 151784 Hom.: 5457 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.251 AC: 38119 AN: 151898 Hom.: 5467 Cov.: 31 AF XY: 0.250 AC XY: 18548 AN XY: 74252

African (AFR) AF: 0.121 AC: 5018 AN: 41406

American (AMR) AF: 0.265 AC: 4035 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1228 AN: 5168

South Asian (SAS) AF: 0.187 AC: 900 AN: 4804

European-Finnish (FIN) AF: 0.323 AC: 3405 AN: 10542

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21664 AN: 67946

Other (OTH) AF: 0.249 AC: 526 AN: 2112

Alfa AF: 0.285 Hom.: 16151

Bravo AF: 0.243

Asia WGS AF: 0.222 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10052004; hg19: chr5-56666500; COSMIC: COSV60136516;