ENST00000750211.1:n.102-12202A>G

Variant names:

• chr9-119886887-T-C
• rs41332646
• ENST00000750211.1:n.102-12202A>G

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.102-12202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 152,114 control chromosomes in the GnomAD database, including 776 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 0.095 (776 hom., cov: 30)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 1 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.102-12202A>G		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.184-12202A>G		intron	N/A
	ENSG00000297691	ENST00000750213.1		n.121-12202A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14392 AN: 151996 Hom.: 777 Cov.: 30

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.00194

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0868

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

GnomAD4 genome AF: 0.0946 AC: 14396 AN: 152114 Hom.: 776 Cov.: 30 AF XY: 0.0897 AC XY: 6670 AN XY: 74338

African (AFR) AF: 0.120 AC: 4980 AN: 41518

American (AMR) AF: 0.0739 AC: 1130 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.00195 AC: 10 AN: 5134

South Asian (SAS) AF: 0.0195 AC: 94 AN: 4814

European-Finnish (FIN) AF: 0.0670 AC: 710 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6997 AN: 67986

Other (OTH) AF: 0.0887 AC: 187 AN: 2108

Alfa AF: 0.105 Hom.: 281

Bravo AF: 0.0970

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs41332646; hg19: chr9-122649165;