9-13755193-T-C

Position:

• chr9-13755193-T-C

Variant summary

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

The ENST00000664438.1(ENSG00000226197):​n.163-81120T>C 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 0.552 in 151,942 control chromosomes in the GnomAD database, including 24,475 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 0.55 (24475 hom., cov: 31)
• Consequence: ENST00000664438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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.163-81120T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83765 AN: 151824 Hom.: 24457 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.552 AC: 83810 AN: 151942 Hom.: 24475 Cov.: 31 AF XY: 0.559 AC XY: 41497 AN XY: 74262

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.556

Alfa AF: 0.592 Hom.: 14411

Bravo AF: 0.541

Asia WGS AF: 0.778 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011531; hg19: chr9-13755192;