9-15104563-G-A

Variant names:

• chr9-15104563-G-A
• rs10756650
• ENST00000609203.1:n.549+21167C>T

Variant summary

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

The ENST00000609203.1(ENSG00000291185):​n.549+21167C>T variant causes a intron 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: ENSG00000291185 ENST00000609203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291185	ENST00000609203.1	TSL:2	n.549+21167C>T		intron	N/A
	ENSG00000291185	ENST00000759520.1		n.97+38422C>T		intron	N/A
	ENSG00000291185	ENST00000759521.1		n.318+41382C>T		intron	N/A

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

African (AFR) AF: 0.396 AC: 16395 AN: 41446

American (AMR) AF: 0.387 AC: 5902 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1278 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1544 AN: 4804

European-Finnish (FIN) AF: 0.318 AC: 3353 AN: 10540

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24231 AN: 67962

Other (OTH) AF: 0.381 AC: 800 AN: 2102

Alfa AF: 0.356 Hom.: 2764

Bravo AF: 0.378

Asia WGS AF: 0.321 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10756650; hg19: chr9-15104561;