9-16962021-G-C

Variant names:

• chr9-16962021-G-C
• rs10511630
• ENST00000649137.2:n.412+3026G>C

Variant summary

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

The ENST00000649137.2(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 ENST00000649137.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 3 publications found

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649137.2. 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
	ENSG00000237153	ENST00000649137.2		n.412+3026G>C		intron	N/A

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

African (AFR) AF: 0.719 AC: 29801 AN: 41466

American (AMR) AF: 0.932 AC: 14241 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3336 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5108 AN: 5170

South Asian (SAS) AF: 0.970 AC: 4682 AN: 4828

European-Finnish (FIN) AF: 0.914 AC: 9687 AN: 10600

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 60987 AN: 68018

Other (OTH) AF: 0.901 AC: 1901 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.071

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: rs10511630;

hg19: chr9-16962019;