chr9-13591907-C-T

Position:

• chr9-13591907-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000664438.1(ENSG00000226197):​n.162+38583C>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 0.141 in 152,062 control chromosomes in the GnomAD database, including 2,049 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 0.14 (2049 hom., cov: 32)
• Consequence: ENST00000664438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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
	ENST00000664438.1	n.162+38583C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21482 AN: 151944 Hom.: 2042 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0716

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.141 AC: 21515 AN: 152062 Hom.: 2049 Cov.: 32 AF XY: 0.135 AC XY: 10019 AN XY: 74352

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0716

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0479

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.141

Alfa AF: 0.114 Hom.: 1472

Bravo AF: 0.152

Asia WGS AF: 0.0610 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	15
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13299116; hg19: chr9-13591906;