rs754848

Variant names:

• chr2-138868219-T-C
• rs754848

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.144 in 152,154 control chromosomes in the GnomAD database, including 2,463 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 0.14 (2463 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.144 AC: 21960 AN: 152036 Hom.: 2459 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.144 AC: 21972 AN: 152154 Hom.: 2463 Cov.: 33 AF XY: 0.140 AC XY: 10413 AN XY: 74380

African (AFR) AF: 0.311 AC: 12901 AN: 41474

American (AMR) AF: 0.0890 AC: 1360 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0663 AC: 320 AN: 4824

European-Finnish (FIN) AF: 0.0694 AC: 736 AN: 10610

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5772 AN: 68006

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.121 Hom.: 312

Bravo AF: 0.153

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	9.8
DANN	Benign	0.88
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs754848; hg19: chr2-139625789;