rs6952272

Variant names:

• chr7-12160434-C-T
• rs6952272

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0447 AC: 1849 AN: 41394

American (AMR) AF: 0.219 AC: 3339 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3466

East Asian (EAS) AF: 0.203 AC: 1043 AN: 5150

South Asian (SAS) AF: 0.209 AC: 1003 AN: 4802

European-Finnish (FIN) AF: 0.152 AC: 1599 AN: 10542

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13413 AN: 67956

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.182 Hom.: 8805

Bravo AF: 0.150

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.56
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6952272; hg19: chr7-12200060;