9-16958702-C-T

Variant names:

• chr9-16958702-C-T
• rs4961430
• ENST00000649137.2:n.327-208C>T

Variant summary

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

The ENST00000649137.2(ENSG00000237153):​n.327-208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,954 control chromosomes in the GnomAD database, including 7,914 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 0.32 (7914 hom., cov: 32)
• Consequence: ENSG00000237153 ENST00000649137.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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.327-208C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48695 AN: 151836 Hom.: 7907 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.321 AC: 48738 AN: 151954 Hom.: 7914 Cov.: 32 AF XY: 0.329 AC XY: 24415 AN XY: 74236

African (AFR) AF: 0.340 AC: 14090 AN: 41426

American (AMR) AF: 0.305 AC: 4657 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2276 AN: 5152

South Asian (SAS) AF: 0.393 AC: 1890 AN: 4806

European-Finnish (FIN) AF: 0.366 AC: 3866 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19924 AN: 67964

Other (OTH) AF: 0.325 AC: 685 AN: 2108

Alfa AF: 0.296 Hom.: 4939

Bravo AF: 0.318

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		-0.46

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: rs4961430;

hg19: chr9-16958700;