chr5-62794435-C-T

Variant names:

• chr5-62794435-C-T
• rs10514947

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 0.0416 in 152,130 control chromosomes in the GnomAD database, including 328 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 0.042 (328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 0 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 = 0.102 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: 0.0416 AC: 6322 AN: 152012 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.00293

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00562

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0416 AC: 6335 AN: 152130 Hom.: 328 Cov.: 32 AF XY: 0.0408 AC XY: 3035 AN XY: 74380

African (AFR) AF: 0.105 AC: 4346 AN: 41472

American (AMR) AF: 0.0518 AC: 792 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3470

East Asian (EAS) AF: 0.0898 AC: 465 AN: 5176

South Asian (SAS) AF: 0.0489 AC: 235 AN: 4808

European-Finnish (FIN) AF: 0.00293 AC: 31 AN: 10592

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00562 AC: 382 AN: 68006

Other (OTH) AF: 0.0346 AC: 73 AN: 2112

Alfa AF: 0.0213 Hom.: 151

Bravo AF: 0.0485

Asia WGS AF: 0.0640 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.44
DANN	Benign	0.18
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10514947; hg19: chr5-62090262;