rs1410713

Variant names:

• chr20-3079704-A-C
• rs1410713

Your query was ambiguous. Multiple possible variants found:

• chr20-3079704-A-C
• chr20-3079704-A-G

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 0.622 in 152,044 control chromosomes in the GnomAD database, including 30,470 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 (30470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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: 0.622 AC: 94565 AN: 151926 Hom.: 30451 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.622 AC: 94632 AN: 152044 Hom.: 30470 Cov.: 32 AF XY: 0.626 AC XY: 46489 AN XY: 74304

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.620

Alfa AF: 0.669 Hom.: 7012

Bravo AF: 0.615

Asia WGS AF: 0.704 AC: 2442 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.8
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410713; hg19: chr20-3060350;