chr5-163244766-C-T

Variant names:

• chr5-163244766-C-T
• rs12153297
• ENST00000503504.2:n.512+12085G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000503504.2(ENSG00000254186):​n.512+12085G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 152,022 control chromosomes in the GnomAD database, including 250 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 0.053 (250 hom., cov: 31)
• Consequence: ENSG00000254186 ENST00000503504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896
• Publications: 3 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1373+12085G>A		intron_variant	Intron 2 of 2
LOC105377700	XR_002956233.2	n.1373+12085G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.2	n.512+12085G>A		intron_variant	Intron 4 of 4	5
ENSG00000254186	ENST00000509211.2	n.527+12085G>A		intron_variant	Intron 4 of 5	3
ENSG00000254186	ENST00000646617.1	n.323-155420G>A		intron_variant	Intron 3 of 14

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8022 AN: 151904 Hom.: 250 Cov.: 31

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0523

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

GnomAD4 genome AF: 0.0528 AC: 8028 AN: 152022 Hom.: 250 Cov.: 31 AF XY: 0.0526 AC XY: 3911 AN XY: 74302

African (AFR) AF: 0.0635 AC: 2636 AN: 41486

American (AMR) AF: 0.0544 AC: 830 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3472

East Asian (EAS) AF: 0.0427 AC: 220 AN: 5154

South Asian (SAS) AF: 0.0445 AC: 214 AN: 4814

European-Finnish (FIN) AF: 0.0504 AC: 533 AN: 10584

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0495 AC: 3363 AN: 67952

Other (OTH) AF: 0.0541 AC: 114 AN: 2108

Alfa AF: 0.0494 Hom.: 247

Bravo AF: 0.0535

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.56
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs12153297; hg19: chr5-162671772;