10-121303660-G-A

Variant names:

• chr10-121303660-G-A
• rs11199884
• ENST00000778913.1:n.176+9556C>T

Variant summary

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

The ENST00000778913.1(ENSG00000301448):​n.176+9556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,026 control chromosomes in the GnomAD database, including 1,095 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 0.11 (1095 hom., cov: 32)
• Consequence: ENSG00000301448 ENST00000778913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

Genes affected

ENSG00000301448 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778913.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301448	ENST00000778913.1		n.176+9556C>T		intron	N/A
	ENSG00000301448	ENST00000778914.1		n.491+9556C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16584 AN: 151908 Hom.: 1094 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.109 AC: 16584 AN: 152026 Hom.: 1095 Cov.: 32 AF XY: 0.110 AC XY: 8149 AN XY: 74300

African (AFR) AF: 0.0367 AC: 1524 AN: 41486

American (AMR) AF: 0.142 AC: 2170 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3470

East Asian (EAS) AF: 0.159 AC: 822 AN: 5156

South Asian (SAS) AF: 0.153 AC: 736 AN: 4800

European-Finnish (FIN) AF: 0.118 AC: 1249 AN: 10550

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8564 AN: 67972

Other (OTH) AF: 0.138 AC: 291 AN: 2106

Alfa AF: 0.115 Hom.: 191

Bravo AF: 0.109

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11199884; hg19: chr10-123063174;