rs2196736

Variant names:

• chr18-78588780-G-A
• rs2196736

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 0.448 in 151,940 control chromosomes in the GnomAD database, including 15,626 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 0.45 (15626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.473 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: 0.448 AC: 68076 AN: 151824 Hom.: 15613 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.448 AC: 68138 AN: 151940 Hom.: 15626 Cov.: 32 AF XY: 0.450 AC XY: 33430 AN XY: 74244

African (AFR) AF: 0.413 AC: 17099 AN: 41408

American (AMR) AF: 0.411 AC: 6285 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1211 AN: 5156

South Asian (SAS) AF: 0.420 AC: 2019 AN: 4802

European-Finnish (FIN) AF: 0.557 AC: 5881 AN: 10556

Middle Eastern (MID) AF: 0.497 AC: 144 AN: 290

European-Non Finnish (NFE) AF: 0.477 AC: 32441 AN: 67954

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.460 Hom.: 45634

Bravo AF: 0.435

Asia WGS AF: 0.359 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2196736; hg19: chr18-76348780;