3-187500548-A-G

Position:

• chr3-187500548-A-G

Variant summary

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

The XR_007096210.1(LOC124909471):​n.111+7218T>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 0.46 in 151,972 control chromosomes in the GnomAD database, including 16,853 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 0.46 (16853 hom., cov: 31)
• Consequence: LOC124909471 XR_007096210.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805

Genes affected

LOC124909471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124909471	XR_007096210.1	n.111+7218T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69847 AN: 151856 Hom.: 16832 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0717

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.460 AC: 69917 AN: 151972 Hom.: 16853 Cov.: 31 AF XY: 0.451 AC XY: 33535 AN XY: 74282

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.0717

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.446

Alfa AF: 0.463 Hom.: 34564

Bravo AF: 0.454

Asia WGS AF: 0.245 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9846911; hg19: chr3-187218336;