rs1864117

Variant names:

• chr5-5818051-G-A
• rs1864117

Your query was ambiguous. Multiple possible variants found:

• chr5-5818051-G-A
• chr5-5818051-G-C

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 0.487 in 151,684 control chromosomes in the GnomAD database, including 18,237 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 0.49 (18237 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.487 AC: 73777 AN: 151564 Hom.: 18227 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.487 AC: 73827 AN: 151684 Hom.: 18237 Cov.: 31 AF XY: 0.489 AC XY: 36251 AN XY: 74094

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.469

Alfa AF: 0.452 Hom.: 33035

Bravo AF: 0.497

Asia WGS AF: 0.570 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1864117; hg19: chr5-5818164;