5-163393889-G-A

Variant names:

• chr5-163393889-G-A
• rs1592778
• ENST00000503504.2:n.375+31914C>T

Variant summary

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

The ENST00000503504.2(ENSG00000254186):​n.375+31914C>T 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 151,944 control chromosomes in the GnomAD database, including 1,529 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 (1529 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000503504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 0 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 = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1236+18430C>T		intron_variant	Intron 1 of 2
LOC105377700	XR_001742965.1	n.1236+18430C>T		intron_variant	Intron 1 of 2
LOC105377700	XR_002956233.2	n.1236+18430C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.2	n.375+31914C>T		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000503615.6	n.351+31914C>T		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000509211.2	n.390+18430C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21073 AN: 151826 Hom.: 1529 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.203

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: 21070 AN: 151944 Hom.: 1529 Cov.: 32 AF XY: 0.141 AC XY: 10453 AN XY: 74266

African (AFR) AF: 0.152 AC: 6286 AN: 41444

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

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3464

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5186

South Asian (SAS) AF: 0.203 AC: 977 AN: 4816

European-Finnish (FIN) AF: 0.163 AC: 1717 AN: 10548

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

European-Non Finnish (NFE) AF: 0.139 AC: 9420 AN: 67926

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.143 Hom.: 216

Bravo AF: 0.131

Asia WGS AF: 0.108 AC: 376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.25
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1592778; hg19: chr5-162820895;