1-73349948-T-G

Position:

• chr1-73349948-T-G

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 0.458 in 151,442 control chromosomes in the GnomAD database, including 16,426 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 (16426 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73349948T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01360	ENST00000415686.6	n.251-5125T>G		intron_variant		2
LINC01360	ENST00000635317.1	n.314-5125T>G		intron_variant		5
LINC01360	ENST00000657455.1	n.428-5125T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69350 AN: 151324 Hom.: 16428 Cov.: 30

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.458 AC: 69368 AN: 151442 Hom.: 16426 Cov.: 30 AF XY: 0.460 AC XY: 34051 AN XY: 74000

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.450

Alfa AF: 0.469 Hom.: 2157

Bravo AF: 0.445

Asia WGS AF: 0.612 AC: 2123 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493515; hg19: chr1-73815631;