chr5-35883702-T-C

Variant names:

• chr5-35883702-T-C
• rs2194225

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 0.447 in 151,982 control chromosomes in the GnomAD database, including 16,297 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 0.45 (16297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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: 0.447 AC: 67957 AN: 151864 Hom.: 16296 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.447 AC: 67974 AN: 151982 Hom.: 16297 Cov.: 32 AF XY: 0.441 AC XY: 32729 AN XY: 74272

African (AFR) AF: 0.611 AC: 25328 AN: 41446

American (AMR) AF: 0.380 AC: 5794 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5170

South Asian (SAS) AF: 0.267 AC: 1284 AN: 4810

European-Finnish (FIN) AF: 0.386 AC: 4080 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27478 AN: 67954

Other (OTH) AF: 0.446 AC: 939 AN: 2104

Alfa AF: 0.421 Hom.: 23076

Bravo AF: 0.458

Asia WGS AF: 0.275 AC: 955 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	2.6
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2194225; hg19: chr5-35883804;