10-87597759-T-C

Variant summary

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

The ENST00000446794.1(ENSG00000223761):n.32-6016A>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 0.727 in 152,058 control chromosomes in the GnomAD database, including 41,427 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 0.73 (41427 hom., cov: 31)
• Consequence: ENST00000446794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378412	XR_946171.2	n.86+1225T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000446794.1	n.32-6016A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110423 AN: 151940 Hom.: 41365 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.727 AC: 110548 AN: 152058 Hom.: 41427 Cov.: 31 AF XY: 0.728 AC XY: 54114 AN XY: 74290

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.718

Alfa AF: 0.645 Hom.: 43429

Bravo AF: 0.734

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.8
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886280; hg19: chr10-89357516;