rs10511606

chr9-15120191-T-C

Variant summary

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

The ENST00000609203.1(ENSG00000291185):n.549+5539A>G 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 0.115 in 152,186 control chromosomes in the GnomAD database, including 1,109 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 0.11 (1109 hom., cov: 32)
• Consequence: ENST00000609203.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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
	ENST00000609203.1	n.549+5539A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17466 AN: 152068 Hom.: 1101 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.115 AC: 17489 AN: 152186 Hom.: 1109 Cov.: 32 AF XY: 0.117 AC XY: 8698 AN XY: 74424

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.109

Alfa AF: 0.106 Hom.: 270

Bravo AF: 0.124

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.77
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511606; hg19: chr9-15120189;