chr5-132053814-T-C

Variant names:

• chr5-132053814-T-C
• rs31400
• ENST00000791953.1:n.296-210A>G

Variant summary

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

The ENST00000791953.1(ENSG00000303119):​n.296-210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,938 control chromosomes in the GnomAD database, including 24,614 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 0.57 (24614 hom., cov: 32)
• Consequence: ENSG00000303119 ENST00000791953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 12 publications found

Genes affected

ENSG00000303119 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379174	XR_001742531.2	n.212-210A>G		intron_variant	Intron 2 of 4
LOC105379174	XR_948785.3	n.229-210A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303119	ENST00000791953.1	n.296-210A>G		intron_variant	Intron 2 of 2
ENSG00000303119	ENST00000791954.1	n.249-210A>G		intron_variant	Intron 2 of 2
ENSG00000303119	ENST00000791955.1	n.237-210A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86049 AN: 151820 Hom.: 24588 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.567 AC: 86124 AN: 151938 Hom.: 24614 Cov.: 32 AF XY: 0.559 AC XY: 41533 AN XY: 74234

African (AFR) AF: 0.596 AC: 24708 AN: 41448

American (AMR) AF: 0.522 AC: 7978 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2828 AN: 5156

South Asian (SAS) AF: 0.395 AC: 1901 AN: 4814

European-Finnish (FIN) AF: 0.550 AC: 5795 AN: 10540

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.579 AC: 39348 AN: 67904

Other (OTH) AF: 0.566 AC: 1197 AN: 2114

Alfa AF: 0.490 Hom.: 2005

Bravo AF: 0.570

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs31400; hg19: chr5-131389507;