5-71718137-C-T

Variant names:

• chr5-71718137-C-T
• rs3857384

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 0.163 in 152,044 control chromosomes in the GnomAD database, including 2,608 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 0.16 (2608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.163 AC: 24798 AN: 151926 Hom.: 2606 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.163 AC: 24819 AN: 152044 Hom.: 2608 Cov.: 32 AF XY: 0.160 AC XY: 11863 AN XY: 74328

African (AFR) AF: 0.297 AC: 12304 AN: 41454

American (AMR) AF: 0.115 AC: 1753 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3470

East Asian (EAS) AF: 0.157 AC: 811 AN: 5166

South Asian (SAS) AF: 0.147 AC: 705 AN: 4798

European-Finnish (FIN) AF: 0.0672 AC: 711 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7416 AN: 67976

Other (OTH) AF: 0.163 AC: 343 AN: 2106

Alfa AF: 0.133 Hom.: 3331

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.57
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3857384; hg19: chr5-71013964;