5-151020023-T-C

Variant names:

• chr5-151020023-T-C
• rs8177404

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 0.149 in 152,146 control chromosomes in the GnomAD database, including 1,790 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 0.15 (1790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22658 AN: 152028 Hom.: 1787 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.149 AC: 22686 AN: 152146 Hom.: 1790 Cov.: 32 AF XY: 0.146 AC XY: 10853 AN XY: 74400

African (AFR) AF: 0.206 AC: 8564 AN: 41496

American (AMR) AF: 0.0951 AC: 1454 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.152 AC: 786 AN: 5170

South Asian (SAS) AF: 0.149 AC: 719 AN: 4814

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10610

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9022 AN: 67986

Other (OTH) AF: 0.137 AC: 289 AN: 2108

Alfa AF: 0.136 Hom.: 3735

Bravo AF: 0.149

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8177404; hg19: chr5-150399584;