2-14665318-G-A

Variant names:

• chr2-14665318-G-A
• rs1434975

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 0.518 in 151,914 control chromosomes in the GnomAD database, including 23,566 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 0.52 (23566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78621 AN: 151796 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.518 AC: 78747 AN: 151914 Hom.: 23566 Cov.: 32 AF XY: 0.517 AC XY: 38344 AN XY: 74230

African (AFR) AF: 0.842 AC: 34943 AN: 41502

American (AMR) AF: 0.471 AC: 7191 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1973 AN: 5124

South Asian (SAS) AF: 0.371 AC: 1790 AN: 4820

European-Finnish (FIN) AF: 0.417 AC: 4398 AN: 10536

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25778 AN: 67896

Other (OTH) AF: 0.486 AC: 1025 AN: 2108

Alfa AF: 0.405 Hom.: 7408

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.51
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1434975; hg19: chr2-14805442;