rs12446238

Variant names:

• chr16-62041234-G-A
• rs12446238

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 0.514 in 151,984 control chromosomes in the GnomAD database, including 21,436 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 0.51 (21436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

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 (AFR) allele frequency at 95% confidence interval = 0.705 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: 0.514 AC: 78081 AN: 151864 Hom.: 21412 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.514 AC: 78140 AN: 151984 Hom.: 21436 Cov.: 32 AF XY: 0.509 AC XY: 37783 AN XY: 74288

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.493

Alfa AF: 0.468 Hom.: 8384

Bravo AF: 0.523

Asia WGS AF: 0.378 AC: 1317 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	1.2
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12446238; hg19: chr16-62075138;