rs12362644

Variant names:

• chr11-64544681-T-C
• rs12362644

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 0.375 in 152,140 control chromosomes in the GnomAD database, including 11,469 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 0.38 (11469 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.375 AC: 57043 AN: 152022 Hom.: 11470 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.375 AC: 57063 AN: 152140 Hom.: 11469 Cov.: 33 AF XY: 0.370 AC XY: 27487 AN XY: 74350

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.375

Alfa AF: 0.409 Hom.: 3250

Bravo AF: 0.365

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12362644; hg19: chr11-64312153;