9-69089911-C-T

Variant summary

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

The ENST00000642330.1(ENSG00000285130):c.385-9990C>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,948 control chromosomes in the GnomAD database, including 9,002 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 0.34 (9002 hom., cov: 32)
• Consequence: ENST00000642330.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642330.1	c.385-9990C>T		intron_variant, NMD_transcript_variant
	ENST00000644977.1	c.*208-9990C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51839 AN: 151828 Hom.: 8999 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.341 AC: 51857 AN: 151948 Hom.: 9002 Cov.: 32 AF XY: 0.342 AC XY: 25371 AN XY: 74280

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.368

Alfa AF: 0.344 Hom.: 5219

Bravo AF: 0.333

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.13
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953588; hg19: chr9-71704827;