1-188359519-C-T

Variant names:

• chr1-188359519-C-T
• rs1387343

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.398 AC: 16470 AN: 41428

American (AMR) AF: 0.414 AC: 6323 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3472

East Asian (EAS) AF: 0.546 AC: 2813 AN: 5152

South Asian (SAS) AF: 0.571 AC: 2753 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4786 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24371 AN: 67952

Other (OTH) AF: 0.379 AC: 799 AN: 2106

Alfa AF: 0.373 Hom.: 33700

Bravo AF: 0.390

Asia WGS AF: 0.568 AC: 1973 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.31
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1387343; hg19: chr1-188328650;