chr9-15104563-G-A

Position:

• chr9-15104563-G-A

Variant summary

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

The ENST00000609203.1(ENSG00000291185):​n.549+21167C>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 0.365 in 151,958 control chromosomes in the GnomAD database, including 10,228 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 0.36 (10228 hom., cov: 32)
• Consequence: ENST00000609203.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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
	ENST00000609203.1	n.549+21167C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55401 AN: 151840 Hom.: 10220 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.365 AC: 55444 AN: 151958 Hom.: 10228 Cov.: 32 AF XY: 0.363 AC XY: 26954 AN XY: 74260

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.381

Alfa AF: 0.355 Hom.: 1145

Bravo AF: 0.378

Asia WGS AF: 0.321 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10756650; hg19: chr9-15104561;