rs7905526

chr10-45055302-T-C

Variant summary

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

The ENST00000456938.6(ENSG00000293022):n.411+10225A>G 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 0.723 in 152,178 control chromosomes in the GnomAD database, including 39,818 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 0.72 (39818 hom., cov: 33)
• Consequence: ENST00000456938.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 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
	ENST00000456938.6	n.411+10225A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000598522.5	n.764+10225A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109885 AN: 152060 Hom.: 39795 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.723 AC: 109957 AN: 152178 Hom.: 39818 Cov.: 33 AF XY: 0.724 AC XY: 53864 AN XY: 74388

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.720

Alfa AF: 0.714 Hom.: 67359

Bravo AF: 0.724

Asia WGS AF: 0.673 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7905526; hg19: chr10-45550750;