rs10506404

Variant names:

• chr12-60013812-T-C
• rs10506404

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 0.0397 in 151,820 control chromosomes in the GnomAD database, including 150 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 0.040 (150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.083 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: 0.0397 AC: 6018 AN: 151702 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0500

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

GnomAD4 genome AF: 0.0397 AC: 6027 AN: 151820 Hom.: 150 Cov.: 32 AF XY: 0.0392 AC XY: 2908 AN XY: 74210

African (AFR) AF: 0.0394 AC: 1637 AN: 41498

American (AMR) AF: 0.0869 AC: 1319 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3466

East Asian (EAS) AF: 0.0531 AC: 272 AN: 5126

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4816

European-Finnish (FIN) AF: 0.00933 AC: 99 AN: 10614

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0358 AC: 2431 AN: 67820

Other (OTH) AF: 0.0495 AC: 104 AN: 2100

Alfa AF: 0.0381 Hom.: 22

Bravo AF: 0.0478

Asia WGS AF: 0.0290 AC: 102 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10506404; hg19: chr12-60407593;