5-163393979-C-G

Variant names:

• chr5-163393979-C-G
• rs1833534
• ENST00000503504.2:n.375+31824G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503504.2(ENSG00000254186):​n.375+31824G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 151,902 control chromosomes in the GnomAD database, including 1,543 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 0.14 (1543 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000503504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 6 publications found

Genes affected

ENSG00000254186 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1236+18340G>C		intron_variant	Intron 1 of 2
LOC105377700	XR_001742965.1	n.1236+18340G>C		intron_variant	Intron 1 of 2
LOC105377700	XR_002956233.2	n.1236+18340G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.2	n.375+31824G>C		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000503615.6	n.351+31824G>C		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000509211.2	n.390+18340G>C		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21107 AN: 151786 Hom.: 1543 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.139 AC: 21107 AN: 151902 Hom.: 1543 Cov.: 32 AF XY: 0.141 AC XY: 10479 AN XY: 74230

African (AFR) AF: 0.152 AC: 6310 AN: 41420

American (AMR) AF: 0.0991 AC: 1511 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3468

East Asian (EAS) AF: 0.0192 AC: 99 AN: 5168

South Asian (SAS) AF: 0.203 AC: 981 AN: 4824

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10544

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9424 AN: 67920

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.0675 Hom.: 87

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.58
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1833534; hg19: chr5-162820985;