5-135896167-T-C

Variant names:

• chr5-135896167-T-C
• rs1799962
• XR_007058947.1:n.*19T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The XR_007058947.1(LOC124901074):​n.*19T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,178 control chromosomes in the GnomAD database, including 421 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 0.071 (421 hom., cov: 32)
• Consequence: LOC124901074 XR_007058947.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.50
• Publications: 9 publications found

Genes affected

LOC124901074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0814 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: 0.0706 AC: 10738 AN: 152060 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0706 AC: 10741 AN: 152178 Hom.: 421 Cov.: 32 AF XY: 0.0715 AC XY: 5321 AN XY: 74414

African (AFR) AF: 0.0794 AC: 3296 AN: 41500

American (AMR) AF: 0.0390 AC: 596 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3462

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0883 AC: 426 AN: 4822

European-Finnish (FIN) AF: 0.0867 AC: 918 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0715 AC: 4864 AN: 68010

Other (OTH) AF: 0.0562 AC: 119 AN: 2116

Alfa AF: 0.0741 Hom.: 154

Bravo AF: 0.0655

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	22
DANN	Benign	0.81
PhyloP100		3.5
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1799962; hg19: chr5-135231856;