rs3024505

Variant names:

• chr1-206766559-G-A
• rs3024505

Your query was ambiguous. Multiple possible variants found:

• chr1-206766559-G-A
• chr1-206766559-G-C
• chr1-206766559-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 0.112 in 152,218 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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: 0.113 AC: 17116 AN: 152098 Hom.: 1196 Cov.: 33

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.112 AC: 17110 AN: 152218 Hom.: 1196 Cov.: 33 AF XY: 0.111 AC XY: 8243 AN XY: 74408

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.0814

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.122

Alfa AF: 0.144 Hom.: 3275

Bravo AF: 0.103

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024505; hg19: chr1-206939904;