rs10511574

chr9-11951204-A-Cchr9-11951204-A-G

Variant summary

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

The ENST00000649122.1(ENSG00000285784):n.388+23265A>C 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 0.0504 in 151,970 control chromosomes in the GnomAD database, including 367 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 0.050 (367 hom., cov: 32)
• Consequence: ENST00000649122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 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
	ENST00000649122.1	n.388+23265A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7651 AN: 151854 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0356

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0504 AC: 7654 AN: 151970 Hom.: 367 Cov.: 32 AF XY: 0.0529 AC XY: 3929 AN XY: 74290

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0356

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0396 Hom.: 111

Bravo AF: 0.0512

Asia WGS AF: 0.120 AC: 416 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511574; hg19: chr9-11951204;