rs41332646

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987122	XR_001746919.2	n.453-12202A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297691	ENST00000750211.1	n.102-12202A>G		intron_variant	Intron 1 of 7
ENSG00000297691	ENST00000750212.1	n.184-12202A>G		intron_variant	Intron 1 of 3
ENSG00000297691	ENST00000750213.1	n.121-12202A>G		intron_variant	Intron 1 of 1

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 v4.3

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;