rs906868

Variant names:

• chr2-30225478-G-T
• rs906868

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.369 AC: 15290 AN: 41430

American (AMR) AF: 0.607 AC: 9270 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1808 AN: 5168

South Asian (SAS) AF: 0.477 AC: 2297 AN: 4818

European-Finnish (FIN) AF: 0.574 AC: 6062 AN: 10564

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42111 AN: 67974

Other (OTH) AF: 0.554 AC: 1168 AN: 2110

Alfa AF: 0.582 Hom.: 14925

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs906868; hg19: chr2-30448344;