4-89858672-A-G

Variant names:

• chr4-89858672-A-G
• rs2737026
• ENST00000776860.1:n.209-17710T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-17710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,020 control chromosomes in the GnomAD database, including 41,762 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 0.74 (41762 hom., cov: 31)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 10 publications found

Genes affected

ENSG00000301182 (HGNC:58852):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301182	ENST00000776860.1		n.209-17710T>C		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-17710T>C		intron	N/A
	ENSG00000301182	ENST00000776862.1		n.81-3626T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112170 AN: 151900 Hom.: 41745 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.738 AC: 112222 AN: 152020 Hom.: 41762 Cov.: 31 AF XY: 0.735 AC XY: 54631 AN XY: 74314

African (AFR) AF: 0.704 AC: 29178 AN: 41442

American (AMR) AF: 0.660 AC: 10060 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2241 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4438 AN: 5166

South Asian (SAS) AF: 0.615 AC: 2955 AN: 4808

European-Finnish (FIN) AF: 0.813 AC: 8610 AN: 10586

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52286 AN: 67976

Other (OTH) AF: 0.716 AC: 1515 AN: 2116

Alfa AF: 0.756 Hom.: 67524

Bravo AF: 0.732

Asia WGS AF: 0.711 AC: 2469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.41
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2737026; hg19: chr4-90779823;