4-89844129-A-G

Variant names:

• chr4-89844129-A-G
• rs1372522
• ENST00000776860.1:n.209-3167T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-3167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,970 control chromosomes in the GnomAD database, including 23,074 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 0.54 (23074 hom., cov: 32)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 9 publications found

Genes affected

ENSG00000301182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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
ENSG00000301182	ENST00000776860.1	n.209-3167T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.183-3167T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.204-3167T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82688 AN: 151850 Hom.: 23069 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.544 AC: 82716 AN: 151970 Hom.: 23074 Cov.: 32 AF XY: 0.544 AC XY: 40392 AN XY: 74274

African (AFR) AF: 0.611 AC: 25309 AN: 41440

American (AMR) AF: 0.481 AC: 7349 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3470

East Asian (EAS) AF: 0.854 AC: 4426 AN: 5182

South Asian (SAS) AF: 0.491 AC: 2369 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6025 AN: 10558

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.502 AC: 34055 AN: 67902

Other (OTH) AF: 0.509 AC: 1073 AN: 2110

Alfa AF: 0.477 Hom.: 6267

Bravo AF: 0.544

Asia WGS AF: 0.650 AC: 2247 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1372522; hg19: chr4-90765280;