rs12668989

Variant names:

• chr7-86032885-T-C
• rs12668989

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 0.138 in 151,328 control chromosomes in the GnomAD database, including 1,493 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 0.14 (1493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 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: 0.138 AC: 20890 AN: 151210 Hom.: 1490 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.138 AC: 20894 AN: 151328 Hom.: 1493 Cov.: 32 AF XY: 0.138 AC XY: 10209 AN XY: 73978

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.159

Alfa AF: 0.149 Hom.: 1055

Bravo AF: 0.140

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12668989; hg19: chr7-85662201;