rs968470

chr2-96757889-T-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 0.452 in 152,172 control chromosomes in the GnomAD database, including 16,903 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 0.45 (16903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68723 AN: 152054 Hom.: 16872 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.452 AC: 68801 AN: 152172 Hom.: 16903 Cov.: 33 AF XY: 0.449 AC XY: 33403 AN XY: 74392

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.397

Alfa AF: 0.394 Hom.: 11924

Bravo AF: 0.451

Asia WGS AF: 0.353 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.18
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs968470; hg19: chr2-97423626;