rs317689

Variant names:

• chr12-69333410-G-A
• rs317689

Your query was ambiguous. Multiple possible variants found:

• chr12-69333410-G-A
• chr12-69333410-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 0.761 in 152,154 control chromosomes in the GnomAD database, including 44,520 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 0.76 (44520 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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: 0.761 AC: 115759 AN: 152036 Hom.: 44477 Cov.: 33

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.761 AC: 115857 AN: 152154 Hom.: 44520 Cov.: 33 AF XY: 0.758 AC XY: 56353 AN XY: 74376

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.735

Alfa AF: 0.725 Hom.: 74877

Bravo AF: 0.766

Asia WGS AF: 0.740 AC: 2575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs317689; hg19: chr12-69727190;