chr4-89844062-C-T

Variant names:

• chr4-89844062-C-T
• rs2870028
• ENST00000776860.1:n.209-3100G>A

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-3100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,724 control chromosomes in the GnomAD database, including 7,983 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 0.31 (7983 hom., cov: 32)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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.209-3100G>A		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.183-3100G>A		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.204-3100G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46323 AN: 151606 Hom.: 7988 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.305 AC: 46311 AN: 151724 Hom.: 7983 Cov.: 32 AF XY: 0.303 AC XY: 22449 AN XY: 74114

African (AFR) AF: 0.154 AC: 6365 AN: 41414

American (AMR) AF: 0.265 AC: 4050 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1116 AN: 3454

East Asian (EAS) AF: 0.302 AC: 1557 AN: 5158

South Asian (SAS) AF: 0.225 AC: 1077 AN: 4792

European-Finnish (FIN) AF: 0.426 AC: 4474 AN: 10506

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26644 AN: 67818

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.335 Hom.: 1216

Bravo AF: 0.287

Asia WGS AF: 0.233 AC: 810 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2870028; hg19: chr4-90765213;