5-99244260-C-G

Variant names:

• chr5-99244260-C-G
• rs17736767

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 0.23 in 152,084 control chromosomes in the GnomAD database, including 4,179 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 0.23 (4179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.230 AC: 34974 AN: 151966 Hom.: 4171 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.230 AC: 35006 AN: 152084 Hom.: 4179 Cov.: 32 AF XY: 0.226 AC XY: 16832 AN XY: 74358

African (AFR) AF: 0.209 AC: 8667 AN: 41496

American (AMR) AF: 0.165 AC: 2523 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.128 AC: 660 AN: 5166

South Asian (SAS) AF: 0.132 AC: 635 AN: 4828

European-Finnish (FIN) AF: 0.248 AC: 2627 AN: 10572

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18256 AN: 67964

Other (OTH) AF: 0.202 AC: 427 AN: 2116

Alfa AF: 0.255 Hom.: 2760

Bravo AF: 0.225

Asia WGS AF: 0.138 AC: 480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.80
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs17736767; hg19: chr5-98579964;