rs12201301

Positions:

• chr6-31039780-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0266 in 152,214 control chromosomes in the GnomAD database, including 72 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 0.027 (72 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0266 (4045/152214) while in subpopulation NFE AF= 0.0295 (2003/68004). AF 95% confidence interval is 0.0284. There are 72 homozygotes in gnomad4. There are 2006 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 72 gene

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: 0.0266 AC: 4044 AN: 152096 Hom.: 72 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0266 AC: 4045 AN: 152214 Hom.: 72 Cov.: 32 AF XY: 0.0270 AC XY: 2006 AN XY: 74398

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.0167

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.0386

Gnomad4 NFE AF: 0.0295

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0303 Hom.: 22

Bravo AF: 0.0266

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12201301; hg19: chr6-31007557;