chr3-120356117-A-G

Position:

• chr3-120356117-A-G

Variant summary

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

The ENST00000494869.2(ENSG00000293512):​n.13+6389A>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 0.455 in 151,994 control chromosomes in the GnomAD database, including 16,102 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 (16102 hom., cov: 32)
• Consequence: ENST00000494869.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC58-DT	XR_007096031.1	n.282+6389A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000494869.2	n.13+6389A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000637360.1	n.280+6389A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69089 AN: 151876 Hom.: 16106 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.455 AC: 69091 AN: 151994 Hom.: 16102 Cov.: 32 AF XY: 0.455 AC XY: 33805 AN XY: 74284

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.416

Alfa AF: 0.469 Hom.: 33991

Bravo AF: 0.434

Asia WGS AF: 0.578 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
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: rs13075278; hg19: chr3-120074964;