12-57681950-T-C

Variant names:

• chr12-57681950-T-C
• rs810204

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 0.617 in 151,412 control chromosomes in the GnomAD database, including 29,215 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 0.62 (29215 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93302 AN: 151294 Hom.: 29203 Cov.: 28

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.617 AC: 93358 AN: 151412 Hom.: 29215 Cov.: 28 AF XY: 0.608 AC XY: 45024 AN XY: 73994

African (AFR) AF: 0.577 AC: 23778 AN: 41226

American (AMR) AF: 0.647 AC: 9848 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2399 AN: 3466

East Asian (EAS) AF: 0.352 AC: 1811 AN: 5144

South Asian (SAS) AF: 0.448 AC: 2146 AN: 4792

European-Finnish (FIN) AF: 0.593 AC: 6176 AN: 10420

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45175 AN: 67838

Other (OTH) AF: 0.650 AC: 1368 AN: 2104

Alfa AF: 0.633 Hom.: 3846

Bravo AF: 0.620

Asia WGS AF: 0.445 AC: 1550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs810204; hg19: chr12-58075733;