rs4740904

chr9-7682860-G-A

Variant summary

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

The XR_007061415.1(LOC124902118):n.598+25100G>A 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 0.468 in 152,030 control chromosomes in the GnomAD database, including 16,682 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 0.47 (16682 hom., cov: 33)
• Consequence: LOC124902118 XR_007061415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19

Genes affected

LOC124902118 (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 (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902118	XR_007061415.1	n.598+25100G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.467 AC: 71017 AN: 151912 Hom.: 16668 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.468 AC: 71085 AN: 152030 Hom.: 16682 Cov.: 33 AF XY: 0.467 AC XY: 34676 AN XY: 74296

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.458

Alfa AF: 0.457 Hom.: 16469

Bravo AF: 0.469

Asia WGS AF: 0.406 AC: 1415 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	0.021
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4740904; hg19: chr9-7682860; COSMIC: COSV69445396;