ENST00000531077.2:n.604-1431C>T

Variant names:

• chr8-60063612-C-T
• rs10504306
• ENST00000531077.2:n.604-1431C>T

Variant summary

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

The ENST00000531077.2(ENSG00000254775):​n.604-1431C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,048 control chromosomes in the GnomAD database, including 292 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 0.037 (292 hom., cov: 32)
• Consequence: ENSG00000254775 ENST00000531077.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 0 publications found

Genes affected

ENSG00000254775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375861	XR_001745714.3	n.502+5084C>T		intron_variant	Intron 3 of 4
LOC105375861	XR_002956710.2	n.502+5084C>T		intron_variant	Intron 3 of 3
LOC105375861	XR_007060918.1	n.225-10982C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254775	ENST00000531077.2	n.604-1431C>T		intron_variant	Intron 4 of 5	3
ENSG00000254775	ENST00000655001.1	n.257-10982C>T		intron_variant	Intron 2 of 3
ENSG00000254775	ENST00000655977.1	n.231-10982C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5643 AN: 151930 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00462

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00185

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0371 AC: 5642 AN: 152048 Hom.: 292 Cov.: 32 AF XY: 0.0377 AC XY: 2799 AN XY: 74332

African (AFR) AF: 0.100 AC: 4167 AN: 41482

American (AMR) AF: 0.0259 AC: 395 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3466

East Asian (EAS) AF: 0.137 AC: 704 AN: 5134

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4826

European-Finnish (FIN) AF: 0.00462 AC: 49 AN: 10614

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00185 AC: 126 AN: 67952

Other (OTH) AF: 0.0308 AC: 65 AN: 2108

Alfa AF: 0.0450 Hom.: 145

Bravo AF: 0.0422

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10504306; hg19: chr8-60976171;