5-1300286-T-C

Variant names:

• chr5-1300286-T-C
• rs2736103

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 0.346 in 152,070 control chromosomes in the GnomAD database, including 9,970 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 0.35 (9970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52628 AN: 151952 Hom.: 9965 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.346 AC: 52669 AN: 152070 Hom.: 9970 Cov.: 32 AF XY: 0.346 AC XY: 25714 AN XY: 74358

African (AFR) AF: 0.193 AC: 8026 AN: 41498

American (AMR) AF: 0.396 AC: 6046 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2167 AN: 5154

South Asian (SAS) AF: 0.532 AC: 2563 AN: 4822

European-Finnish (FIN) AF: 0.286 AC: 3030 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28011 AN: 67958

Other (OTH) AF: 0.395 AC: 832 AN: 2104

Alfa AF: 0.391 Hom.: 8265

Bravo AF: 0.346

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.23
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2736103; hg19: chr5-1300401;