rs10506638

Positions:

• chr12-71600397-T-C

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 0.0582 in 152,260 control chromosomes in the GnomAD database, including 359 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 0.058 (359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0809 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: 0.0582 AC: 8857 AN: 152142 Hom.: 359 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0582 AC: 8863 AN: 152260 Hom.: 359 Cov.: 32 AF XY: 0.0593 AC XY: 4413 AN XY: 74444

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0608

Gnomad4 ASJ AF: 0.0698

Gnomad4 EAS AF: 0.00404

Gnomad4 SAS AF: 0.0878

Gnomad4 FIN AF: 0.0926

Gnomad4 NFE AF: 0.0776

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0726 Hom.: 68

Bravo AF: 0.0524

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506638; hg19: chr12-71994177;