5-98594262-C-T

Variant names:

• chr5-98594262-C-T
• rs461409

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 0.356 in 152,000 control chromosomes in the GnomAD database, including 10,393 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 0.36 (10393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54046 AN: 151882 Hom.: 10388 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.356 AC: 54074 AN: 152000 Hom.: 10393 Cov.: 32 AF XY: 0.346 AC XY: 25709 AN XY: 74302

African (AFR) AF: 0.493 AC: 20429 AN: 41468

American (AMR) AF: 0.286 AC: 4367 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3468

East Asian (EAS) AF: 0.157 AC: 811 AN: 5170

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4824

European-Finnish (FIN) AF: 0.220 AC: 2326 AN: 10558

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22255 AN: 67944

Other (OTH) AF: 0.354 AC: 745 AN: 2102

Alfa AF: 0.341 Hom.: 28616

Bravo AF: 0.371

Asia WGS AF: 0.250 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.48
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs461409; hg19: chr5-97929966;