rs1708080

Variant names:

• chr3-39566270-G-A
• rs1708080

Your query was ambiguous. Multiple possible variants found:

• chr3-39566270-G-A
• chr3-39566270-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 0.743 in 152,084 control chromosomes in the GnomAD database, including 43,355 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 0.74 (43355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.743 AC: 112921 AN: 151966 Hom.: 43346 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.743 AC: 112965 AN: 152084 Hom.: 43355 Cov.: 32 AF XY: 0.744 AC XY: 55323 AN XY: 74334

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.782

Alfa AF: 0.781 Hom.: 5902

Bravo AF: 0.733

Asia WGS AF: 0.793 AC: 2747 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1708080; hg19: chr3-39607761;