7-24294450-A-G

Variant summary

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

The XR_001745132.2(LOC107986777):n.209+24907T>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 0.924 in 152,290 control chromosomes in the GnomAD database, including 65,120 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 0.92 (65120 hom., cov: 33)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

LOC107986777 (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 (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+24907T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140675 AN: 152172 Hom.: 65069 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.955

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.924 AC: 140783 AN: 152290 Hom.: 65120 Cov.: 33 AF XY: 0.924 AC XY: 68827 AN XY: 74454

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.929

Alfa AF: 0.921 Hom.: 88544

Bravo AF: 0.931

Asia WGS AF: 0.932 AC: 3243 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	8.5
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16472; hg19: chr7-24334069;