rs2221338

Variant names:

• chr2-67997613-G-A
• rs2221338

Your query was ambiguous. Multiple possible variants found:

• chr2-67997613-G-A
• chr2-67997613-G-C
• chr2-67997613-G-T

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 0.122 in 152,102 control chromosomes in the GnomAD database, including 2,073 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 0.12 (2073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.122 AC: 18487 AN: 151984 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.122 AC: 18521 AN: 152102 Hom.: 2073 Cov.: 32 AF XY: 0.120 AC XY: 8941 AN XY: 74368

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.0811

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.0698 Hom.: 692

Bravo AF: 0.137

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2221338; hg19: chr2-68224745;