rs699549

Variant names:

• chr2-4657673-T-C
• rs699549

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 0.854 in 152,170 control chromosomes in the GnomAD database, including 55,966 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 0.85 (55966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 5 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 = 0.951 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129882 AN: 152052 Hom.: 55902 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.854 AC: 130008 AN: 152170 Hom.: 55966 Cov.: 32 AF XY: 0.852 AC XY: 63364 AN XY: 74390

African (AFR) AF: 0.958 AC: 39820 AN: 41546

American (AMR) AF: 0.891 AC: 13631 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3867 AN: 5160

South Asian (SAS) AF: 0.765 AC: 3691 AN: 4826

European-Finnish (FIN) AF: 0.801 AC: 8443 AN: 10538

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55505 AN: 68008

Other (OTH) AF: 0.843 AC: 1783 AN: 2114

Alfa AF: 0.826 Hom.: 186049

Bravo AF: 0.866

Asia WGS AF: 0.745 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs699549; hg19: chr2-4705263;