7-24295105-A-G

Position:

• chr7-24295105-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+24252T>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 0.506 in 152,042 control chromosomes in the GnomAD database, including 19,885 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 0.51 (19885 hom., cov: 32)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986777	XR_001745132.2	n.209+24252T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76909 AN: 151924 Hom.: 19875 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.506 AC: 76957 AN: 152042 Hom.: 19885 Cov.: 32 AF XY: 0.511 AC XY: 37939 AN XY: 74296

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.509

Alfa AF: 0.518 Hom.: 4256

Bravo AF: 0.511

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16120; hg19: chr7-24334724;