rs12667992

Positions:

• chr7-91715762-G-A

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 0.129 in 152,046 control chromosomes in the GnomAD database, including 1,376 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 0.13 (1376 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91715762G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTERF1	ENST00000454222.5	n.160-22303C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19557 AN: 151926 Hom.: 1379 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.129 AC: 19570 AN: 152046 Hom.: 1376 Cov.: 31 AF XY: 0.132 AC XY: 9823 AN XY: 74324

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.134

Alfa AF: 0.110 Hom.: 2062

Bravo AF: 0.131

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12667992; hg19: chr7-91345077;