chr2-79084647-C-T

Variant names:

• chr2-79084647-C-T
• rs7583314

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 0.515 in 151,882 control chromosomes in the GnomAD database, including 20,529 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 (20529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 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: 0.515 AC: 78192 AN: 151764 Hom.: 20521 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.515 AC: 78221 AN: 151882 Hom.: 20529 Cov.: 32 AF XY: 0.512 AC XY: 37992 AN XY: 74214

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.469

Alfa AF: 0.535 Hom.: 19150

Bravo AF: 0.509

Asia WGS AF: 0.454 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7583314; hg19: chr2-79311773;