5-131948917-C-T

Variant names:

• chr5-131948917-C-T
• rs477086
• ENST00000652469.1:n.2032-1255G>A

Variant summary

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

The ENST00000652469.1(ENSG00000281938):​n.2032-1255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,996 control chromosomes in the GnomAD database, including 11,185 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 0.35 (11185 hom., cov: 32)
• Consequence: ENSG00000281938 ENST00000652469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 8 publications found

Genes affected

ENSG00000281938 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000281938	ENST00000652469.1	n.2032-1255G>A		intron_variant	Intron 20 of 25			ENSP00000498837.1
ENSG00000281938	ENST00000413683.5	n.1957-1255G>A		intron_variant	Intron 19 of 30	2		ENSP00000415140.1
ENSG00000234758	ENST00000446275.1	n.117+4393C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53638 AN: 151880 Hom.: 11154 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.353 AC: 53721 AN: 151996 Hom.: 11185 Cov.: 32 AF XY: 0.354 AC XY: 26272 AN XY: 74272

African (AFR) AF: 0.585 AC: 24239 AN: 41444

American (AMR) AF: 0.315 AC: 4808 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2507 AN: 5164

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4820

European-Finnish (FIN) AF: 0.296 AC: 3118 AN: 10544

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15571 AN: 67962

Other (OTH) AF: 0.314 AC: 664 AN: 2112

Alfa AF: 0.278 Hom.: 4773

Bravo AF: 0.368

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.094
DANN	Benign	0.25
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs477086; hg19: chr5-131284610;