2-96122160-G-C

Variant names:

• chr2-96122160-G-C
• rs1168965

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 0.286 in 152,062 control chromosomes in the GnomAD database, including 6,990 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 0.29 (6990 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.286 AC: 43476 AN: 151944 Hom.: 6983 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.286 AC: 43516 AN: 152062 Hom.: 6990 Cov.: 33 AF XY: 0.291 AC XY: 21622 AN XY: 74314

African (AFR) AF: 0.162 AC: 6722 AN: 41474

American (AMR) AF: 0.293 AC: 4476 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2201 AN: 5152

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4816

European-Finnish (FIN) AF: 0.465 AC: 4926 AN: 10586

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22440 AN: 67956

Other (OTH) AF: 0.253 AC: 535 AN: 2114

Alfa AF: 0.311 Hom.: 991

Bravo AF: 0.274

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs1168965; hg19: chr2-96787899;