chr1-90744429-T-C

Variant names:

• chr1-90744429-T-C
• rs1526480
• ENST00000759598.1:n.285+20211T>C

Variant summary

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

The ENST00000759598.1(ENSG00000287076):​n.285+20211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,942 control chromosomes in the GnomAD database, including 13,506 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 0.42 (13506 hom., cov: 32)
• Consequence: ENSG00000287076 ENST00000759598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 8 publications found

Genes affected

ENSG00000287076 (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 (AMR) allele frequency at 95% confidence interval = 0.461 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
ENSG00000287076	ENST00000759598.1	n.285+20211T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63374 AN: 151822 Hom.: 13467 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.418 AC: 63473 AN: 151942 Hom.: 13506 Cov.: 32 AF XY: 0.428 AC XY: 31763 AN XY: 74290

African (AFR) AF: 0.413 AC: 17089 AN: 41422

American (AMR) AF: 0.471 AC: 7180 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1970 AN: 5162

South Asian (SAS) AF: 0.425 AC: 2045 AN: 4812

European-Finnish (FIN) AF: 0.590 AC: 6240 AN: 10570

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26315 AN: 67932

Other (OTH) AF: 0.406 AC: 857 AN: 2112

Alfa AF: 0.392 Hom.: 16854

Bravo AF: 0.411

Asia WGS AF: 0.440 AC: 1531 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	0.51
DANN	Benign	0.40
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1526480; hg19: chr1-91209986;