1-189892274-A-T

Variant names:

• chr1-189892274-A-T
• rs1400544

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

The variant allele was found at a frequency of 0.287 in 152,040 control chromosomes in the GnomAD database, including 6,975 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 (6975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 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: 0.287 AC: 43572 AN: 151922 Hom.: 6959 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.287 AC: 43617 AN: 152040 Hom.: 6975 Cov.: 32 AF XY: 0.285 AC XY: 21147 AN XY: 74272

African (AFR) AF: 0.429 AC: 17798 AN: 41468

American (AMR) AF: 0.210 AC: 3212 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1036 AN: 3472

East Asian (EAS) AF: 0.152 AC: 788 AN: 5168

South Asian (SAS) AF: 0.309 AC: 1492 AN: 4828

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 100 AN: 288

European-Non Finnish (NFE) AF: 0.237 AC: 16102 AN: 67960

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.260 Hom.: 719

Bravo AF: 0.290

Asia WGS AF: 0.235 AC: 809 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.47
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1400544; hg19: chr1-189861404;