rs6952272

Positions:

• chr7-12160434-C-T

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 0.154 in 151,884 control chromosomes in the GnomAD database, including 2,233 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 0.15 (2233 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 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: 0.154 AC: 23432 AN: 151764 Hom.: 2236 Cov.: 30

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.154 AC: 23431 AN: 151884 Hom.: 2233 Cov.: 30 AF XY: 0.156 AC XY: 11594 AN XY: 74226

Gnomad4 AFR AF: 0.0447

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.148

Alfa AF: 0.192 Hom.: 5867

Bravo AF: 0.150

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6952272; hg19: chr7-12200060;