8-121501931-T-C

Variant names:

• chr8-121501931-T-C
• rs13261248
• ENST00000784704.1:n.285+28724T>C

Variant summary

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

The ENST00000784704.1(ENSG00000302156):​n.285+28724T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,104 control chromosomes in the GnomAD database, including 22,308 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 0.49 (22308 hom., cov: 32)
• Consequence: ENSG00000302156 ENST00000784704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 3 publications found

Genes affected

ENSG00000302156 (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 = 0.859 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
ENSG00000302156	ENST00000784704.1	n.285+28724T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73948 AN: 151986 Hom.: 22252 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.487 AC: 74047 AN: 152104 Hom.: 22308 Cov.: 32 AF XY: 0.481 AC XY: 35750 AN XY: 74354

African (AFR) AF: 0.866 AC: 35958 AN: 41518

American (AMR) AF: 0.403 AC: 6161 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1412 AN: 5174

South Asian (SAS) AF: 0.435 AC: 2097 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 3006 AN: 10584

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22562 AN: 67954

Other (OTH) AF: 0.444 AC: 937 AN: 2112

Alfa AF: 0.380 Hom.: 13718

Bravo AF: 0.507

Asia WGS AF: 0.372 AC: 1297 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	0.68
DANN	Benign	0.64
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs13261248; hg19: chr8-122514171;