2-68023164-G-T

Variant names:

• chr2-68023164-G-T
• rs7558466

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.561 in 151,876 control chromosomes in the GnomAD database, including 24,508 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 0.56 (24508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.561 AC: 85133 AN: 151758 Hom.: 24473 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.561 AC: 85225 AN: 151876 Hom.: 24508 Cov.: 31 AF XY: 0.562 AC XY: 41673 AN XY: 74202

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.586

Alfa AF: 0.509 Hom.: 41599

Bravo AF: 0.570

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7558466; hg19: chr2-68250296;