9-26755932-T-C

Position:

• chr9-26755932-T-C

Variant summary

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

The ENST00000523363.1(ENSG00000254261):​n.354+7620T>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 0.236 in 152,122 control chromosomes in the GnomAD database, including 5,838 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 0.24 (5838 hom., cov: 33)
• Consequence: ENST00000523363.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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
	ENST00000523363.1	n.354+7620T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35777 AN: 152004 Hom.: 5825 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.236 AC: 35830 AN: 152122 Hom.: 5838 Cov.: 33 AF XY: 0.235 AC XY: 17475 AN XY: 74376

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0717

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.212

Alfa AF: 0.161 Hom.: 3029

Bravo AF: 0.240

Asia WGS AF: 0.226 AC: 788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10283761; hg19: chr9-26755930;