rs10491753

chr9-13545787-A-C

Variant summary

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

The ENST00000664438.1(ENSG00000226197):n.113-7488A>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 0.0498 in 152,290 control chromosomes in the GnomAD database, including 277 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 (277 hom., cov: 32)
• Consequence: ENST00000664438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

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 (NFE) allele frequency at 95% confidence interval = 0.0753 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
	ENST00000664438.1	n.113-7488A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7598 AN: 152172 Hom.: 277 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0498 AC: 7591 AN: 152290 Hom.: 277 Cov.: 32 AF XY: 0.0466 AC XY: 3466 AN XY: 74456

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.0513

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.0770

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0670 Hom.: 178

Bravo AF: 0.0497

Asia WGS AF: 0.0140 AC: 47 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.33
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491753; hg19: chr9-13545786;