rs12700667

Variant names:

• chr7-25862019-G-A
• rs12700667

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 0.623 in 152,008 control chromosomes in the GnomAD database, including 31,319 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 0.62 (31319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 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: 0.624 AC: 94720 AN: 151890 Hom.: 31324 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.623 AC: 94744 AN: 152008 Hom.: 31319 Cov.: 32 AF XY: 0.619 AC XY: 45988 AN XY: 74294

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.648

Alfa AF: 0.701 Hom.: 35602

Bravo AF: 0.611

Asia WGS AF: 0.402 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
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: rs12700667; hg19: chr7-25901639;