rs10511606

Variant names:

• chr9-15120191-T-C
• rs10511606
• ENST00000609203.1:n.549+5539A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609203.1(ENSG00000291185):​n.549+5539A>G variant causes a intron 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: ENSG00000291185 ENST00000609203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 3 publications found

Genes affected

ENSG00000291185 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609203.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291185	ENST00000609203.1	TSL:2	n.549+5539A>G		intron	N/A
	ENSG00000291185	ENST00000759520.1		n.97+22794A>G		intron	N/A
	ENSG00000291185	ENST00000759521.1		n.318+25754A>G		intron	N/A

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

African (AFR) AF: 0.118 AC: 4913 AN: 41534

American (AMR) AF: 0.170 AC: 2602 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1083 AN: 5170

South Asian (SAS) AF: 0.154 AC: 744 AN: 4820

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6628 AN: 67988

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.113 Hom.: 499

Bravo AF: 0.124

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.77
DANN	Benign	0.51
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs10511606; hg19: chr9-15120189;