5-134501370-T-G

Variant names:

• chr5-134501370-T-G
• rs1476097
• ENST00000773017.1:n.75-8831A>C

Variant summary

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

The ENST00000773017.1(ENSG00000300625):​n.75-8831A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,066 control chromosomes in the GnomAD database, including 13,253 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 0.41 (13253 hom., cov: 33)
• Consequence: ENSG00000300625 ENST00000773017.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 2 publications found

Genes affected

ENSG00000300625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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
ENSG00000300625	ENST00000773017.1	n.75-8831A>C		intron_variant	Intron 1 of 3
ENSG00000300625	ENST00000773018.1	n.150-8831A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62114 AN: 151948 Hom.: 13234 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.409 AC: 62191 AN: 152066 Hom.: 13253 Cov.: 33 AF XY: 0.416 AC XY: 30886 AN XY: 74332

African (AFR) AF: 0.504 AC: 20926 AN: 41484

American (AMR) AF: 0.368 AC: 5626 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2817 AN: 5174

South Asian (SAS) AF: 0.474 AC: 2287 AN: 4820

European-Finnish (FIN) AF: 0.453 AC: 4788 AN: 10574

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22994 AN: 67958

Other (OTH) AF: 0.390 AC: 823 AN: 2112

Alfa AF: 0.358 Hom.: 35135

Bravo AF: 0.406

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1476097; hg19: chr5-133837061;