chr5-143483675-C-T

Variant names:

• chr5-143483675-C-T
• rs7721458

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 0.109 in 151,362 control chromosomes in the GnomAD database, including 1,299 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 0.11 (1299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.109 AC: 16478 AN: 151244 Hom.: 1298 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.0452

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 16484 AN: 151362 Hom.: 1299 Cov.: 32 AF XY: 0.116 AC XY: 8594 AN XY: 73894

African (AFR) AF: 0.0880 AC: 3638 AN: 41326

American (AMR) AF: 0.0957 AC: 1451 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 579 AN: 3456

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5164

South Asian (SAS) AF: 0.104 AC: 498 AN: 4808

European-Finnish (FIN) AF: 0.209 AC: 2171 AN: 10386

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.0964 AC: 6533 AN: 67762

Other (OTH) AF: 0.109 AC: 229 AN: 2094

Alfa AF: 0.143 Hom.: 977

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs7721458; hg19: chr5-142863240; COSMIC: COSV60203253;