rs273849

Positions:

• chr12-60727464-A-G
• chr12-60727464-A-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 0.355 in 151,796 control chromosomes in the GnomAD database, including 14,907 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 0.36 (14907 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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: 0.355 AC: 53851 AN: 151676 Hom.: 14858 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.355 AC: 53958 AN: 151796 Hom.: 14907 Cov.: 31 AF XY: 0.351 AC XY: 26084 AN XY: 74220

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.297

Alfa AF: 0.126 Hom.: 297

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs273849; hg19: chr12-61121245;