chr9-16958702-C-T

Variant names:

• chr9-16958702-C-T
• rs4961430
• ENST00000649137.1:n.327-208C>T

Variant summary

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

The ENST00000649137.1(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 ENST00000649137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.327-208C>T		intron_variant	Intron 4 of 7

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

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.325

Alfa AF: 0.289 Hom.: 3313

Bravo AF: 0.318

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961430; hg19: chr9-16958700;