rs968470

Variant names:

• chr2-96757889-T-C
• rs968470

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 0.452 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.641 AC: 26601 AN: 41524

American (AMR) AF: 0.320 AC: 4891 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2010 AN: 5172

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4830

European-Finnish (FIN) AF: 0.485 AC: 5143 AN: 10598

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26708 AN: 67968

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.396 Hom.: 14016

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs968470; hg19: chr2-97423626;