rs968470

Variant names:

• chr2-96757889-T-C
• rs968470

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;