2-96157242-T-C

Variant names:

• chr2-96157242-T-C
• rs1168969

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 0.81 in 152,212 control chromosomes in the GnomAD database, including 50,803 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 0.81 (50803 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.810 AC: 123155 AN: 152094 Hom.: 50732 Cov.: 33

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.810 AC: 123289 AN: 152212 Hom.: 50803 Cov.: 33 AF XY: 0.812 AC XY: 60458 AN XY: 74438

African (AFR) AF: 0.952 AC: 39545 AN: 41560

American (AMR) AF: 0.797 AC: 12188 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2427 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5156 AN: 5164

South Asian (SAS) AF: 0.940 AC: 4539 AN: 4828

European-Finnish (FIN) AF: 0.748 AC: 7936 AN: 10606

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48900 AN: 67966

Other (OTH) AF: 0.791 AC: 1672 AN: 2114

Alfa AF: 0.772 Hom.: 5671

Bravo AF: 0.821

Asia WGS AF: 0.965 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.6
DANN	Benign	0.81
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1168969; hg19: chr2-96822981;