rs754848

Variant names:

• chr2-138868219-T-C
• rs754848

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.135

Alfa AF: 0.115 Hom.: 270

Bravo AF: 0.153

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754848; hg19: chr2-139625789;