chr1-191658152-G-A

Variant names:

• chr1-191658152-G-A
• rs1338034

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 0.676 in 152,002 control chromosomes in the GnomAD database, including 35,413 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 0.68 (35413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102692 AN: 151884 Hom.: 35351 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.676 AC: 102809 AN: 152002 Hom.: 35413 Cov.: 32 AF XY: 0.678 AC XY: 50364 AN XY: 74280

African (AFR) AF: 0.816 AC: 33858 AN: 41492

American (AMR) AF: 0.685 AC: 10455 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2241 AN: 3472

East Asian (EAS) AF: 0.569 AC: 2941 AN: 5170

South Asian (SAS) AF: 0.682 AC: 3292 AN: 4826

European-Finnish (FIN) AF: 0.623 AC: 6564 AN: 10542

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41321 AN: 67930

Other (OTH) AF: 0.661 AC: 1396 AN: 2112

Alfa AF: 0.626 Hom.: 103528

Bravo AF: 0.685

Asia WGS AF: 0.646 AC: 2244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1338034; hg19: chr1-191627282; COSMIC: COSV60004192;