rs7976955

chr12-5948811-G-Achr12-5948811-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 0.174 in 632,192 control chromosomes in the GnomAD database, including 10,443 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 0.18 (2563 hom., cov: 33)
  • Exomes 𝑓: 0.17 (7880 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27003 AN: 152076 Hom.: 2557 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.172 AC: 82764 AN: 479996 Hom.: 7880 AF XY: 0.178 AC XY: 45150 AN XY: 253402

Gnomad4 AFR exome AF: 0.213

Gnomad4 AMR exome AF: 0.133

Gnomad4 ASJ exome AF: 0.159

Gnomad4 EAS exome AF: 0.0233

Gnomad4 SAS exome AF: 0.261

Gnomad4 FIN exome AF: 0.138

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.178 AC: 27032 AN: 152196 Hom.: 2563 Cov.: 33 AF XY: 0.174 AC XY: 12944 AN XY: 74420

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0291

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.162

Alfa AF: 0.117 Hom.: 270

Bravo AF: 0.180

Asia WGS AF: 0.136 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.19
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7976955; hg19: chr12-6057977;