7-12248292-A-T

Variant names:

• chr7-12248292-A-T
• rs6952078

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 0.211 in 152,112 control chromosomes in the GnomAD database, including 5,604 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 0.21 (5604 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32039 AN: 151994 Hom.: 5592 Cov.: 33

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.211 AC: 32101 AN: 152112 Hom.: 5604 Cov.: 33 AF XY: 0.208 AC XY: 15464 AN XY: 74368

African (AFR) AF: 0.479 AC: 19861 AN: 41442

American (AMR) AF: 0.110 AC: 1681 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.153 AC: 791 AN: 5182

South Asian (SAS) AF: 0.195 AC: 938 AN: 4816

European-Finnish (FIN) AF: 0.0624 AC: 662 AN: 10604

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7110 AN: 68004

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.0417 Hom.: 47

Bravo AF: 0.226

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6952078; hg19: chr7-12287918;