rs1341974

Variant names:

• chr1-189908801-G-A
• rs1341974

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 0.273 in 151,934 control chromosomes in the GnomAD database, including 6,160 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 0.27 (6160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.273 AC: 41494 AN: 151818 Hom.: 6150 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.273 AC: 41525 AN: 151934 Hom.: 6160 Cov.: 32 AF XY: 0.272 AC XY: 20166 AN XY: 74236

African (AFR) AF: 0.384 AC: 15923 AN: 41452

American (AMR) AF: 0.200 AC: 3049 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3466

East Asian (EAS) AF: 0.151 AC: 784 AN: 5178

South Asian (SAS) AF: 0.307 AC: 1481 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10556

Middle Eastern (MID) AF: 0.343 AC: 98 AN: 286

European-Non Finnish (NFE) AF: 0.237 AC: 16091 AN: 67890

Other (OTH) AF: 0.259 AC: 545 AN: 2104

Alfa AF: 0.257 Hom.: 1037

Bravo AF: 0.274

Asia WGS AF: 0.232 AC: 798 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.16
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1341974; hg19: chr1-189877931;