chr4-89863377-A-G

Variant names:

• chr4-89863377-A-G
• rs2736994
• ENST00000776860.1:n.209-22415T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-22415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 151,934 control chromosomes in the GnomAD database, including 47,032 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 0.79 (47032 hom., cov: 30)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 14 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776860.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301182	ENST00000776860.1		n.209-22415T>C		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-22415T>C		intron	N/A
	ENSG00000301182	ENST00000776862.1		n.81-8331T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119290 AN: 151816 Hom.: 46985 Cov.: 30

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.786 AC: 119387 AN: 151934 Hom.: 47032 Cov.: 30 AF XY: 0.783 AC XY: 58096 AN XY: 74236

African (AFR) AF: 0.802 AC: 33250 AN: 41444

American (AMR) AF: 0.741 AC: 11308 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2466 AN: 3472

East Asian (EAS) AF: 0.776 AC: 3979 AN: 5128

South Asian (SAS) AF: 0.662 AC: 3172 AN: 4794

European-Finnish (FIN) AF: 0.830 AC: 8762 AN: 10554

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53857 AN: 67968

Other (OTH) AF: 0.776 AC: 1638 AN: 2110

Alfa AF: 0.789 Hom.: 10752

Bravo AF: 0.785

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2736994; hg19: chr4-90784528;