ENST00000649137.1:n.412+3026G>C

Variant names:

• chr9-16962021-G-C
• rs10511630
• ENST00000649137.1:n.412+3026G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649137.1(ENSG00000237153):​n.412+3026G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,154 control chromosomes in the GnomAD database, including 56,886 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 0.86 (56886 hom., cov: 32)
• Consequence: ENSG00000237153 ENST00000649137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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
ENSG00000237153	ENST00000649137.1	n.412+3026G>C		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130804 AN: 152036 Hom.: 56860 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.860 AC: 130876 AN: 152154 Hom.: 56886 Cov.: 32 AF XY: 0.865 AC XY: 64380 AN XY: 74386

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.901

Alfa AF: 0.872 Hom.: 6799

Bravo AF: 0.855

Asia WGS AF: 0.962 AC: 3347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511630; hg19: chr9-16962019;