rs12197235

Variant names:

• chr6-252772-C-T
• rs12197235

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 0.198 in 152,140 control chromosomes in the GnomAD database, including 3,505 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 0.20 (3505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.321 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30002 AN: 152024 Hom.: 3478 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.198 AC: 30062 AN: 152140 Hom.: 3505 Cov.: 32 AF XY: 0.198 AC XY: 14763 AN XY: 74390

African (AFR) AF: 0.326 AC: 13502 AN: 41478

American (AMR) AF: 0.221 AC: 3383 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3472

East Asian (EAS) AF: 0.256 AC: 1325 AN: 5180

South Asian (SAS) AF: 0.129 AC: 621 AN: 4828

European-Finnish (FIN) AF: 0.126 AC: 1335 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8950 AN: 67994

Other (OTH) AF: 0.185 AC: 392 AN: 2114

Alfa AF: 0.173 Hom.: 460

Bravo AF: 0.211

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.71
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12197235; hg19: chr6-252772;