10-119201190-A-G

Variant names:

• chr10-119201190-A-G
• rs11198819
• ENST00000826909.1:n.259-5127A>G

Variant summary

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

The ENST00000826909.1(ENSG00000307533):​n.259-5127A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 113,854 control chromosomes in the GnomAD database, including 9,209 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 0.45 (9209 hom., cov: 29)
• Consequence: ENSG00000307533 ENST00000826909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 16 publications found

Genes affected

ENSG00000307533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826909.1. 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
	ENSG00000307533	ENST00000826909.1		n.259-5127A>G		intron	N/A
	ENSG00000307533	ENST00000826910.1		n.137-1415A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 51444 AN: 113726 Hom.: 9196 Cov.: 29

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.452 AC: 51503 AN: 113854 Hom.: 9209 Cov.: 29 AF XY: 0.453 AC XY: 25078 AN XY: 55412

African (AFR) AF: 0.476 AC: 18075 AN: 37986

American (AMR) AF: 0.371 AC: 3814 AN: 10270

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1124 AN: 2432

East Asian (EAS) AF: 0.579 AC: 2608 AN: 4508

South Asian (SAS) AF: 0.405 AC: 1289 AN: 3184

European-Finnish (FIN) AF: 0.463 AC: 3270 AN: 7058

Middle Eastern (MID) AF: 0.419 AC: 88 AN: 210

European-Non Finnish (NFE) AF: 0.439 AC: 20215 AN: 46034

Other (OTH) AF: 0.441 AC: 661 AN: 1500

Alfa AF: 0.301 Hom.: 13371

Bravo AF: 0.344

Asia WGS AF: 0.362 AC: 1256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.29
PhyloP100		-0.79

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: rs11198819;

hg19: chr10-120960702;