rs2717055

Variant names:

• chr2-57817085-G-A
• rs2717055

Your query was ambiguous. Multiple possible variants found:

• chr2-57817085-G-A
• chr2-57817085-G-C
• chr2-57817085-G-T

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 0.616 in 151,726 control chromosomes in the GnomAD database, including 28,767 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 0.62 (28767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 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: 0.616 AC: 93339 AN: 151608 Hom.: 28744 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.616 AC: 93420 AN: 151726 Hom.: 28767 Cov.: 32 AF XY: 0.615 AC XY: 45590 AN XY: 74142

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.622

Alfa AF: 0.603 Hom.: 4650

Bravo AF: 0.609

Asia WGS AF: 0.602 AC: 2086 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2717055; hg19: chr2-58044220;