2-79108467-C-T

Variant names:

• chr2-79108467-C-T
• rs283863

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 0.97 in 151,382 control chromosomes in the GnomAD database, including 71,220 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 0.97 (71220 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.970 AC: 146672 AN: 151260 Hom.: 71158 Cov.: 29

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.970 AC: 146795 AN: 151382 Hom.: 71220 Cov.: 29 AF XY: 0.972 AC XY: 71881 AN XY: 73984

African (AFR) AF: 0.991 AC: 40506 AN: 40856

American (AMR) AF: 0.975 AC: 14856 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3325 AN: 3462

East Asian (EAS) AF: 1.00 AC: 5165 AN: 5166

South Asian (SAS) AF: 0.988 AC: 4752 AN: 4810

European-Finnish (FIN) AF: 0.968 AC: 10244 AN: 10580

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64775 AN: 67956

Other (OTH) AF: 0.968 AC: 2037 AN: 2104

Alfa AF: 0.967 Hom.: 8660

Bravo AF: 0.969

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.70
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs283863; hg19: chr2-79335593;