4-89843548-C-T

Variant names:

• chr4-89843548-C-T
• rs7687945
• ENST00000776860.1:n.209-2586G>A

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-2586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,916 control chromosomes in the GnomAD database, including 24,787 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 0.56 (24787 hom., cov: 32)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 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.209-2586G>A		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-2586G>A		intron	N/A
	ENSG00000301182	ENST00000776862.1		n.204-2586G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85691 AN: 151800 Hom.: 24780 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.564 AC: 85724 AN: 151916 Hom.: 24787 Cov.: 32 AF XY: 0.564 AC XY: 41893 AN XY: 74242

African (AFR) AF: 0.640 AC: 26528 AN: 41468

American (AMR) AF: 0.544 AC: 8308 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3468

East Asian (EAS) AF: 0.855 AC: 4433 AN: 5186

South Asian (SAS) AF: 0.526 AC: 2530 AN: 4810

European-Finnish (FIN) AF: 0.573 AC: 6031 AN: 10532

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34486 AN: 67890

Other (OTH) AF: 0.537 AC: 1128 AN: 2100

Alfa AF: 0.517 Hom.: 6307

Bravo AF: 0.569

Asia WGS AF: 0.675 AC: 2337 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7687945; hg19: chr4-90764699;