rs4521068

Variant names:

• chr2-238943130-G-A
• rs4521068

Your query was ambiguous. Multiple possible variants found:

• chr2-238943130-G-A
• chr2-238943130-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.164 in 152,170 control chromosomes in the GnomAD database, including 2,587 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 0.16 (2587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.164 AC: 24938 AN: 152054 Hom.: 2589 Cov.: 32

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.164 AC: 24926 AN: 152170 Hom.: 2587 Cov.: 32 AF XY: 0.165 AC XY: 12258 AN XY: 74396

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.178

Alfa AF: 0.204 Hom.: 6795

Bravo AF: 0.155

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4521068; hg19: chr2-239864826;