rs12668989

Positions:

• chr7-86032885-T-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 0.138 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;