rs2736107

chr5-1297739-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.231 in 152,106 control chromosomes in the GnomAD database, including 4,697 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 0.23 (4697 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

ACMG classification

Verdict is Benign. Variant got -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 = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35101 AN: 151988 Hom.: 4688 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.231 AC: 35122 AN: 152106 Hom.: 4697 Cov.: 33 AF XY: 0.229 AC XY: 17054 AN XY: 74350

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.269

Alfa AF: 0.171 Hom.: 593

Bravo AF: 0.227

Asia WGS AF: 0.403 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.8
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736107; hg19: chr5-1297854;