1-196218535-G-A

Variant names:

• chr1-196218535-G-A
• rs1998712

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 0.715 in 152,102 control chromosomes in the GnomAD database, including 42,140 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 0.71 (42140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.715 AC: 108677 AN: 151984 Hom.: 42133 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.715 AC: 108718 AN: 152102 Hom.: 42140 Cov.: 32 AF XY: 0.721 AC XY: 53618 AN XY: 74354

African (AFR) AF: 0.383 AC: 15864 AN: 41436

American (AMR) AF: 0.795 AC: 12154 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3123 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4886 AN: 5170

South Asian (SAS) AF: 0.866 AC: 4181 AN: 4828

European-Finnish (FIN) AF: 0.839 AC: 8886 AN: 10588

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56961 AN: 68002

Other (OTH) AF: 0.732 AC: 1545 AN: 2110

Alfa AF: 0.807 Hom.: 215276

Bravo AF: 0.698

Asia WGS AF: 0.846 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
DANN	Benign	0.38
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs1998712; hg19: chr1-196187665;