7-24308107-G-C

Position:

• chr7-24308107-G-C

Variant summary

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

The XR_001745132.2(LOC107986777):​n.209+11250C>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 0.454 in 151,866 control chromosomes in the GnomAD database, including 15,881 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 0.45 (15881 hom., cov: 32)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+11250C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68868 AN: 151748 Hom.: 15883 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.454 AC: 68887 AN: 151866 Hom.: 15881 Cov.: 32 AF XY: 0.450 AC XY: 33372 AN XY: 74186

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.445

Alfa AF: 0.476 Hom.: 2129

Bravo AF: 0.446

Asia WGS AF: 0.275 AC: 960 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	16
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16091; hg19: chr7-24347726;