rs2735845

Variant names:

• chr5-1300469-C-G
• rs2735845

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 0.167 in 152,242 control chromosomes in the GnomAD database, including 2,475 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 0.17 (2475 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.167 AC: 25351 AN: 152124 Hom.: 2469 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.167 AC: 25372 AN: 152242 Hom.: 2475 Cov.: 33 AF XY: 0.170 AC XY: 12629 AN XY: 74432

African (AFR) AF: 0.0748 AC: 3110 AN: 41552

American (AMR) AF: 0.209 AC: 3200 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1675 AN: 5178

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1715 AN: 10598

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12967 AN: 68008

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.174 Hom.: 366

Bravo AF: 0.163

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.8
DANN	Benign	0.43
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2735845; hg19: chr5-1300584;