4-89854061-A-G

Variant names:

• chr4-89854061-A-G
• rs10516848
• ENST00000776860.1:n.209-13099T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-13099T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,124 control chromosomes in the GnomAD database, including 8,622 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 0.33 (8622 hom., cov: 33)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 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.209-13099T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.183-13099T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.203+863T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49446 AN: 152002 Hom.: 8625 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.325 AC: 49445 AN: 152124 Hom.: 8622 Cov.: 33 AF XY: 0.322 AC XY: 23951 AN XY: 74338

African (AFR) AF: 0.222 AC: 9228 AN: 41534

American (AMR) AF: 0.271 AC: 4134 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1083 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4494 AN: 10548

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26749 AN: 67978

Other (OTH) AF: 0.300 AC: 634 AN: 2114

Alfa AF: 0.373 Hom.: 15205

Bravo AF: 0.310

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.39
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10516848; hg19: chr4-90775212;