chr2-17807391-A-C

Variant names:

• chr2-17807391-A-C
• rs214034

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 0.702 in 151,894 control chromosomes in the GnomAD database, including 38,134 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 0.70 (38134 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.702 AC: 106589 AN: 151776 Hom.: 38091 Cov.: 30

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.702 AC: 106692 AN: 151894 Hom.: 38134 Cov.: 30 AF XY: 0.706 AC XY: 52421 AN XY: 74200

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.694

Alfa AF: 0.497 Hom.: 944

Bravo AF: 0.716

Asia WGS AF: 0.915 AC: 3176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs214034; hg19: chr2-17988658;