chr5-135896167-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901074	XR_007058947.1	n.*19T>C		downstream_gene_variant

Ensembl

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

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 v4.3

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;