2-85950199-T-C

Variant names:

• chr2-85950199-T-C
• rs735738

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 0.424 in 151,948 control chromosomes in the GnomAD database, including 14,869 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 0.42 (14869 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 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: 0.424 AC: 64365 AN: 151830 Hom.: 14864 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.424 AC: 64391 AN: 151948 Hom.: 14869 Cov.: 31 AF XY: 0.419 AC XY: 31110 AN XY: 74278

African (AFR) AF: 0.285 AC: 11821 AN: 41426

American (AMR) AF: 0.373 AC: 5694 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3468

East Asian (EAS) AF: 0.111 AC: 574 AN: 5164

South Asian (SAS) AF: 0.412 AC: 1978 AN: 4806

European-Finnish (FIN) AF: 0.464 AC: 4901 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 36069 AN: 67944

Other (OTH) AF: 0.428 AC: 901 AN: 2106

Alfa AF: 0.486 Hom.: 58112

Bravo AF: 0.405

Asia WGS AF: 0.262 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.65
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs735738; hg19: chr2-86177322;