rs10756650

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-15104563-G-A
• chr9-15104563-G-T

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 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

Genes affected

ENSG00000291185 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291185	ENST00000609203.1	n.549+21167C>T		intron_variant	Intron 2 of 9	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;