chr1-188339158-C-T

Variant names:

• chr1-188339158-C-T
• rs4434808

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 0.291 in 152,026 control chromosomes in the GnomAD database, including 6,905 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 0.29 (6905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44224 AN: 151908 Hom.: 6901 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.291 AC: 44258 AN: 152026 Hom.: 6905 Cov.: 32 AF XY: 0.299 AC XY: 22225 AN XY: 74310

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.262

Alfa AF: 0.237 Hom.: 5798

Bravo AF: 0.294

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4434808; hg19: chr1-188308289;