rs317689

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;