8-114490872-G-A

Variant names:

• chr8-114490872-G-A
• rs10505218
• ENST00000776828.1:n.235+13414C>T

Variant summary

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

The ENST00000776828.1(ENSG00000301177):​n.235+13414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 151,764 control chromosomes in the GnomAD database, including 271 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 0.042 (271 hom., cov: 32)
• Consequence: ENSG00000301177 ENST00000776828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 0 publications found

Genes affected

ENSG00000301177 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0954 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
ENSG00000301177	ENST00000776828.1	n.235+13414C>T		intron_variant	Intron 1 of 3
ENSG00000301177	ENST00000776829.1	n.247+13414C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0416 AC: 6301 AN: 151646 Hom.: 265 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0417 AC: 6336 AN: 151764 Hom.: 271 Cov.: 32 AF XY: 0.0420 AC XY: 3117 AN XY: 74212

African (AFR) AF: 0.0980 AC: 4059 AN: 41434

American (AMR) AF: 0.0497 AC: 755 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3464

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4822

European-Finnish (FIN) AF: 0.0269 AC: 285 AN: 10582

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0150 AC: 1014 AN: 67788

Other (OTH) AF: 0.0427 AC: 90 AN: 2110

Alfa AF: 0.0316 Hom.: 44

Bravo AF: 0.0448

Asia WGS AF: 0.0140 AC: 47 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs10505218; hg19: chr8-115503101;