8-24924066-G-C

Position:

• chr8-24924066-G-C

Variant summary

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

The XR_002956698.2(LOC112268023):​n.121+524C>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 0.526 in 152,054 control chromosomes in the GnomAD database, including 24,321 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 0.53 (24321 hom., cov: 32)
• Consequence: LOC112268023 XR_002956698.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

LOC112268023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268023	XR_002956698.2	n.121+524C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80024 AN: 151936 Hom.: 24311 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.526 AC: 80053 AN: 152054 Hom.: 24321 Cov.: 32 AF XY: 0.530 AC XY: 39401 AN XY: 74334

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.537

Alfa AF: 0.577 Hom.: 3419

Bravo AF: 0.516

Asia WGS AF: 0.629 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1379357; hg19: chr8-24781579;