10-9007290-C-T

Variant names:

• chr10-9007290-C-T
• rs12413578
• ENST00000798219.1:n.260+11407G>A

Variant summary

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

The ENST00000798219.1(ENSG00000303941):​n.260+11407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 151,920 control chromosomes in the GnomAD database, including 522 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 0.072 (522 hom., cov: 31)
• Consequence: ENSG00000303941 ENST00000798219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 33 publications found

Genes affected

ENSG00000303941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798219.1. 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
	ENSG00000303941	ENST00000798219.1		n.260+11407G>A		intron	N/A
	ENSG00000303941	ENST00000798220.1		n.329+11407G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10914 AN: 151804 Hom.: 524 Cov.: 31

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0122

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0718 AC: 10913 AN: 151920 Hom.: 522 Cov.: 31 AF XY: 0.0698 AC XY: 5179 AN XY: 74230

African (AFR) AF: 0.0195 AC: 808 AN: 41442

American (AMR) AF: 0.0833 AC: 1271 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3472

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5158

South Asian (SAS) AF: 0.0852 AC: 410 AN: 4810

European-Finnish (FIN) AF: 0.0506 AC: 531 AN: 10492

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6941 AN: 67970

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0845 Hom.: 1205

Bravo AF: 0.0727

Asia WGS AF: 0.0460 AC: 161 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-1.0

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: rs12413578;

hg19: chr10-9049253;