1-188359519-C-T

Position:

• chr1-188359519-C-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 0.395 in 151,958 control chromosomes in the GnomAD database, including 12,071 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 0.39 (12071 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.188359519C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59925 AN: 151840 Hom.: 12066 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.395 AC: 59961 AN: 151958 Hom.: 12071 Cov.: 32 AF XY: 0.402 AC XY: 29870 AN XY: 74274

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.379

Alfa AF: 0.372 Hom.: 21785

Bravo AF: 0.390

Asia WGS AF: 0.568 AC: 1973 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387343; hg19: chr1-188328650;