3-146185639-G-T

Position:

• chr3-146185639-G-T

Variant summary

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

The variant allele was found at a frequency of 0.115 in 151,966 control chromosomes in the GnomAD database, including 1,033 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 0.11 (1033 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.146185639G>T		intergenic_region
LOC105374145	XR_001740949.2	n.740+4160C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17420 AN: 151850 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.115 AC: 17440 AN: 151966 Hom.: 1033 Cov.: 32 AF XY: 0.114 AC XY: 8434 AN XY: 74290

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0346

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.118

Alfa AF: 0.117 Hom.: 1392

Bravo AF: 0.112

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11928424; hg19: chr3-145903426;