rs10506638

Variant names:

• chr12-71600397-T-C
• rs10506638

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 0.0582 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
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.0809 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: 0.0582 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

African (AFR) AF: 0.0190 AC: 791 AN: 41554

American (AMR) AF: 0.0608 AC: 931 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3466

East Asian (EAS) AF: 0.00404 AC: 21 AN: 5192

South Asian (SAS) AF: 0.0878 AC: 423 AN: 4820

European-Finnish (FIN) AF: 0.0926 AC: 981 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5279 AN: 68008

Other (OTH) AF: 0.0525 AC: 111 AN: 2116

Alfa AF: 0.0716 Hom.: 69

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10506638; hg19: chr12-71994177;