chr5-35588987-C-T

Variant names:

• chr5-35588987-C-T
• rs4703415

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 0.249 in 152,078 control chromosomes in the GnomAD database, including 5,922 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 0.25 (5922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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: 0.249 AC: 37771 AN: 151958 Hom.: 5897 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.249 AC: 37854 AN: 152078 Hom.: 5922 Cov.: 32 AF XY: 0.253 AC XY: 18836 AN XY: 74340

African (AFR) AF: 0.392 AC: 16244 AN: 41482

American (AMR) AF: 0.306 AC: 4676 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.456 AC: 2351 AN: 5160

South Asian (SAS) AF: 0.384 AC: 1850 AN: 4820

European-Finnish (FIN) AF: 0.158 AC: 1678 AN: 10590

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10030 AN: 67970

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.173 Hom.: 2651

Bravo AF: 0.269

Asia WGS AF: 0.414 AC: 1438 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4703415; hg19: chr5-35589089;