chr5-103587233-G-C

Variant names:

• chr5-103587233-G-C
• rs10515347

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 0.334 in 151,730 control chromosomes in the GnomAD database, including 8,645 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 0.33 (8645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.334 AC: 50670 AN: 151610 Hom.: 8641 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.334 AC: 50686 AN: 151730 Hom.: 8645 Cov.: 32 AF XY: 0.330 AC XY: 24419 AN XY: 74092

African (AFR) AF: 0.294 AC: 12168 AN: 41426

American (AMR) AF: 0.314 AC: 4786 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1330 AN: 3470

East Asian (EAS) AF: 0.180 AC: 928 AN: 5164

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3326 AN: 10506

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25210 AN: 67798

Other (OTH) AF: 0.333 AC: 702 AN: 2106

Alfa AF: 0.212 Hom.: 457

Bravo AF: 0.332

Asia WGS AF: 0.263 AC: 909 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.3
DANN	Benign	0.51
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10515347; hg19: chr5-102922934;