5-175433696-T-C

Variant names:

• chr5-175433696-T-C
• rs265973

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 0.572 in 152,026 control chromosomes in the GnomAD database, including 25,099 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 0.57 (25099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 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: 0.572 AC: 86849 AN: 151908 Hom.: 25076 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.572 AC: 86919 AN: 152026 Hom.: 25099 Cov.: 32 AF XY: 0.571 AC XY: 42416 AN XY: 74320

African (AFR) AF: 0.629 AC: 26106 AN: 41476

American (AMR) AF: 0.620 AC: 9485 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2878 AN: 5162

South Asian (SAS) AF: 0.421 AC: 2024 AN: 4810

European-Finnish (FIN) AF: 0.516 AC: 5441 AN: 10536

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37143 AN: 67964

Other (OTH) AF: 0.586 AC: 1239 AN: 2114

Alfa AF: 0.559 Hom.: 51373

Bravo AF: 0.585

Asia WGS AF: 0.476 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs265973; hg19: chr5-174860699; COSMIC: COSV60236681;