rs12204500

Positions:

• chr6-31108620-T-A

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 0.127 in 152,036 control chromosomes in the GnomAD database, including 1,335 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 0.13 (1335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.127 AC: 19305 AN: 151918 Hom.: 1328 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.127 AC: 19327 AN: 152036 Hom.: 1335 Cov.: 32 AF XY: 0.128 AC XY: 9504 AN XY: 74332

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0996

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.131

Alfa AF: 0.115 Hom.: 166

Bravo AF: 0.130

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12204500; hg19: chr6-31076397;