rs906868

Variant names:

• chr2-30225478-G-T
• rs906868

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 0.532 in 152,022 control chromosomes in the GnomAD database, including 22,570 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 0.53 (22570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 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: 0.533 AC: 80906 AN: 151904 Hom.: 22562 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.532 AC: 80947 AN: 152022 Hom.: 22570 Cov.: 32 AF XY: 0.530 AC XY: 39395 AN XY: 74304

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.554

Alfa AF: 0.581 Hom.: 13406

Bravo AF: 0.532

Asia WGS AF: 0.408 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs906868; hg19: chr2-30448344;