10-31079550-T-C

Variant summary

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

The ENST00000658872.1(ENSG00000287564):n.323-26389T>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 0.801 in 152,206 control chromosomes in the GnomAD database, including 48,973 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 0.80 (48973 hom., cov: 33)
• Consequence: ENST00000658872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376481	XR_001747410.3	n.2795-26389T>C		intron_variant, non_coding_transcript_variant
LOC105376481	XR_001747409.3	n.2795-26389T>C		intron_variant, non_coding_transcript_variant
LOC105376481	XR_930796.3	n.904-26389T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658872.1	n.323-26389T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121806 AN: 152088 Hom.: 48934 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.801 AC: 121906 AN: 152206 Hom.: 48973 Cov.: 33 AF XY: 0.802 AC XY: 59713 AN XY: 74416

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.793

Alfa AF: 0.808 Hom.: 9268

Bravo AF: 0.805

Asia WGS AF: 0.769 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.5
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1771628; hg19: chr10-31368479;