chr5-109333253-C-T

Variant names:

• chr5-109333253-C-T
• rs2435061

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 0.566 in 152,050 control chromosomes in the GnomAD database, including 27,658 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 (27658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85961 AN: 151932 Hom.: 27604 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.566 AC: 86072 AN: 152050 Hom.: 27658 Cov.: 32 AF XY: 0.568 AC XY: 42202 AN XY: 74344

African (AFR) AF: 0.856 AC: 35541 AN: 41510

American (AMR) AF: 0.528 AC: 8048 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3470

East Asian (EAS) AF: 0.951 AC: 4926 AN: 5180

South Asian (SAS) AF: 0.431 AC: 2077 AN: 4816

European-Finnish (FIN) AF: 0.429 AC: 4527 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27765 AN: 67944

Other (OTH) AF: 0.518 AC: 1094 AN: 2112

Alfa AF: 0.497 Hom.: 3431

Bravo AF: 0.589

Asia WGS AF: 0.712 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2435061; hg19: chr5-108668954; COSMIC: COSV63272202;