ENST00000649415.2:n.341+6652C>G

Variant names:

• chr11-39154873-G-C
• rs10837120
• ENST00000649415.2:n.341+6652C>G

Variant summary

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

The ENST00000649415.2(ENSG00000285751):​n.341+6652C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,834 control chromosomes in the GnomAD database, including 26,163 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 0.58 (26163 hom., cov: 32)
• Consequence: ENSG00000285751 ENST00000649415.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 0 publications found

Genes affected

ENSG00000285751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285751	ENST00000649415.2	n.341+6652C>G		intron_variant	Intron 1 of 2
ENSG00000285751	ENST00000722718.1	n.343+6652C>G		intron_variant	Intron 1 of 5
ENSG00000285751	ENST00000722719.1	n.133-4006C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87541 AN: 151716 Hom.: 26149 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.577 AC: 87593 AN: 151834 Hom.: 26163 Cov.: 32 AF XY: 0.580 AC XY: 43046 AN XY: 74158

African (AFR) AF: 0.418 AC: 17321 AN: 41418

American (AMR) AF: 0.676 AC: 10322 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2218 AN: 3462

East Asian (EAS) AF: 0.821 AC: 4231 AN: 5156

South Asian (SAS) AF: 0.636 AC: 3069 AN: 4822

European-Finnish (FIN) AF: 0.530 AC: 5585 AN: 10530

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42759 AN: 67874

Other (OTH) AF: 0.619 AC: 1306 AN: 2110

Alfa AF: 0.584 Hom.: 3349

Bravo AF: 0.581

Asia WGS AF: 0.725 AC: 2511 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10837120; hg19: chr11-39176423;