5-175445317-A-G

Variant names:

• chr5-175445317-A-G
• rs10078866

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 0.0545 in 152,168 control chromosomes in the GnomAD database, including 438 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 0.054 (438 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.0545 AC: 8288 AN: 152052 Hom.: 437 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0545 AC: 8290 AN: 152168 Hom.: 438 Cov.: 33 AF XY: 0.0554 AC XY: 4119 AN XY: 74416

African (AFR) AF: 0.110 AC: 4545 AN: 41452

American (AMR) AF: 0.0462 AC: 708 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1053 AN: 5134

South Asian (SAS) AF: 0.113 AC: 545 AN: 4830

European-Finnish (FIN) AF: 0.0194 AC: 206 AN: 10630

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0150 AC: 1018 AN: 68018

Other (OTH) AF: 0.0549 AC: 116 AN: 2114

Alfa AF: 0.0151 Hom.: 14

Bravo AF: 0.0600

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		-0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10078866;

hg19: chr5-174872320;