rs10519705

Variant names:

• chr5-122520776-G-C
• rs10519705

Your query was ambiguous. Multiple possible variants found:

• chr5-122520776-G-C
• chr5-122520776-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 0.0258 in 152,174 control chromosomes in the GnomAD database, including 97 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 0.026 (97 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.057 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: 0.0258 AC: 3917 AN: 152058 Hom.: 97 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.00332

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0258 AC: 3925 AN: 152174 Hom.: 97 Cov.: 32 AF XY: 0.0252 AC XY: 1875 AN XY: 74396

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0133

Gnomad4 OTH AF: 0.0198

Alfa AF: 0.00676 Hom.: 2

Bravo AF: 0.0283

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519705; hg19: chr5-121856471;