9-16958702-C-T

Position:

• chr9-16958702-C-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, non coding transcript 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: ENST00000649137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649137.1	n.327-208C>T		intron_variant, non_coding_transcript_variant

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;