5-105745334-T-C

Variant names:

• chr5-105745334-T-C
• rs4543241

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 0.314 in 151,916 control chromosomes in the GnomAD database, including 8,247 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 0.31 (8247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47617 AN: 151798 Hom.: 8242 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.314 AC: 47646 AN: 151916 Hom.: 8247 Cov.: 31 AF XY: 0.320 AC XY: 23725 AN XY: 74238

African (AFR) AF: 0.176 AC: 7285 AN: 41424

American (AMR) AF: 0.431 AC: 6569 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1395 AN: 5148

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4812

European-Finnish (FIN) AF: 0.391 AC: 4130 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23746 AN: 67944

Other (OTH) AF: 0.326 AC: 687 AN: 2106

Alfa AF: 0.344 Hom.: 5229

Bravo AF: 0.309

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.77
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4543241; hg19: chr5-105081035;