rs10516849

Variant names:

• chr4-89868388-A-G
• rs10516849
• ENST00000776860.1:n.209-27426T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-27426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,186 control chromosomes in the GnomAD database, including 2,012 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 0.13 (2012 hom., cov: 32)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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.209-27426T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.182+26931T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.81-13342T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20516 AN: 152068 Hom.: 2007 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0702

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.135 AC: 20539 AN: 152186 Hom.: 2012 Cov.: 32 AF XY: 0.133 AC XY: 9913 AN XY: 74410

African (AFR) AF: 0.265 AC: 11005 AN: 41488

American (AMR) AF: 0.0785 AC: 1200 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1630 AN: 5176

South Asian (SAS) AF: 0.112 AC: 538 AN: 4822

European-Finnish (FIN) AF: 0.0579 AC: 614 AN: 10612

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0702 AC: 4776 AN: 68014

Other (OTH) AF: 0.139 AC: 293 AN: 2106

Alfa AF: 0.0915 Hom.: 3526

Bravo AF: 0.143

Asia WGS AF: 0.224 AC: 777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.68
DANN	Benign	0.74
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10516849; hg19: chr4-90789539;