3-150337774-G-T

Position:

• chr3-150337774-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 0.161 in 151,820 control chromosomes in the GnomAD database, including 3,081 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 0.16 (3081 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150337774G>T		intergenic_region
LOC107986141	XR_001740958.1	n.1982-9604G>T		intron_variant
LOC107986141	XR_007096127.1	n.1982-9604G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24349 AN: 151702 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.161 AC: 24411 AN: 151820 Hom.: 3081 Cov.: 32 AF XY: 0.156 AC XY: 11554 AN XY: 74218

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0941

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0834 Hom.: 274

Bravo AF: 0.172

Asia WGS AF: 0.0600 AC: 208 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1597466; hg19: chr3-150055561;