2-83677335-T-C

Variant names:

• chr2-83677335-T-C
• rs1551196

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 0.945 in 152,130 control chromosomes in the GnomAD database, including 68,154 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 0.95 (68154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.972 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: 0.945 AC: 143693 AN: 152012 Hom.: 68113 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.945 AC: 143787 AN: 152130 Hom.: 68154 Cov.: 32 AF XY: 0.943 AC XY: 70118 AN XY: 74374

African (AFR) AF: 0.884 AC: 36684 AN: 41486

American (AMR) AF: 0.972 AC: 14863 AN: 15286

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3469 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4768 AN: 5176

South Asian (SAS) AF: 0.837 AC: 4033 AN: 4818

European-Finnish (FIN) AF: 0.967 AC: 10238 AN: 10584

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66543 AN: 67990

Other (OTH) AF: 0.951 AC: 2012 AN: 2116

Alfa AF: 0.959 Hom.: 8513

Bravo AF: 0.946

Asia WGS AF: 0.863 AC: 2995 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.68
DANN	Benign	0.56
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1551196; hg19: chr2-83904459;