5-98743276-C-T

Variant names:

• chr5-98743276-C-T
• rs12652843

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 0.261 in 152,008 control chromosomes in the GnomAD database, including 5,464 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 0.26 (5464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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: 0.261 AC: 39691 AN: 151890 Hom.: 5463 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.261 AC: 39719 AN: 152008 Hom.: 5464 Cov.: 32 AF XY: 0.257 AC XY: 19094 AN XY: 74298

African (AFR) AF: 0.217 AC: 8988 AN: 41450

American (AMR) AF: 0.243 AC: 3714 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3466

East Asian (EAS) AF: 0.0914 AC: 473 AN: 5174

South Asian (SAS) AF: 0.264 AC: 1274 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2084 AN: 10550

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20781 AN: 67940

Other (OTH) AF: 0.274 AC: 579 AN: 2114

Alfa AF: 0.302 Hom.: 11161

Bravo AF: 0.265

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.36
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs12652843; hg19: chr5-98078980;