12-37953836-G-T

Variant names:

• chr12-37953836-G-T
• rs8186746

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 0.389 in 151,186 control chromosomes in the GnomAD database, including 12,967 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 0.39 (12967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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: 0.390 AC: 58871 AN: 151068 Hom.: 12967 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.0999

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.389 AC: 58886 AN: 151186 Hom.: 12967 Cov.: 32 AF XY: 0.383 AC XY: 28286 AN XY: 73836

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.426

Alfa AF: 0.485 Hom.: 16905

Bravo AF: 0.373

Asia WGS AF: 0.206 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8186746; hg19: chr12-38347638;