5-84788958-C-T

Variant names:

• chr5-84788958-C-T
• rs113524839

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 0.0587 in 152,252 control chromosomes in the GnomAD database, including 362 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 0.059 (362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8938 AN: 152134 Hom.: 362 Cov.: 32

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0587 AC: 8942 AN: 152252 Hom.: 362 Cov.: 32 AF XY: 0.0576 AC XY: 4288 AN XY: 74416

African (AFR) AF: 0.0163 AC: 677 AN: 41572

American (AMR) AF: 0.0640 AC: 978 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0816 AC: 283 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5176

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4820

European-Finnish (FIN) AF: 0.0598 AC: 634 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0852 AC: 5794 AN: 68002

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0470 Hom.: 129

Bravo AF: 0.0566

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.36
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs113524839; hg19: chr5-84084776;