rs2736107

Variant names:

• chr5-1297739-C-T
• rs2736107

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 0.231 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
• Publications: 18 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 = 0.494 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: 0.231 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

African (AFR) AF: 0.123 AC: 5102 AN: 41498

American (AMR) AF: 0.219 AC: 3348 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1395 AN: 5160

South Asian (SAS) AF: 0.510 AC: 2461 AN: 4822

European-Finnish (FIN) AF: 0.157 AC: 1663 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19044 AN: 67972

Other (OTH) AF: 0.269 AC: 569 AN: 2112

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2736107; hg19: chr5-1297854;