rs12173570

Positions:

• chr6-151636579-C-T

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 0.203 in 152,064 control chromosomes in the GnomAD database, including 5,177 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 (5177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

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: 0.203 AC: 30833 AN: 151946 Hom.: 5163 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.203 AC: 30876 AN: 152064 Hom.: 5177 Cov.: 32 AF XY: 0.197 AC XY: 14675 AN XY: 74324

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.199

Alfa AF: 0.116 Hom.: 1393

Bravo AF: 0.223

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12173570; hg19: chr6-151957714;