5-132023306-T-C

Variant names:

• chr5-132023306-T-C
• rs3846726

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 0.501 in 151,778 control chromosomes in the GnomAD database, including 19,251 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 (19251 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.501 AC: 76047 AN: 151660 Hom.: 19244 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.501 AC: 76091 AN: 151778 Hom.: 19251 Cov.: 30 AF XY: 0.495 AC XY: 36691 AN XY: 74186

African (AFR) AF: 0.517 AC: 21356 AN: 41332

American (AMR) AF: 0.477 AC: 7291 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2776 AN: 5136

South Asian (SAS) AF: 0.313 AC: 1503 AN: 4798

European-Finnish (FIN) AF: 0.478 AC: 5056 AN: 10570

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34771 AN: 67890

Other (OTH) AF: 0.505 AC: 1064 AN: 2106

Alfa AF: 0.495 Hom.: 9522

Bravo AF: 0.508

Asia WGS AF: 0.438 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.60
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3846726; hg19: chr5-131358999;