rs7297967

Positions:

• chr12-667205-G-A
• chr12-667205-G-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 0.564 in 152,042 control chromosomes in the GnomAD database, including 24,238 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 0.56 (24238 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.564 AC: 85706 AN: 151924 Hom.: 24205 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.564 AC: 85785 AN: 152042 Hom.: 24238 Cov.: 33 AF XY: 0.568 AC XY: 42206 AN XY: 74338

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.549

Alfa AF: 0.556 Hom.: 4606

Bravo AF: 0.557

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.67
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7297967; hg19: chr12-776371;