rs6582630

chr12-38349706-G-Achr12-38349706-G-T

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 0.62 in 151,820 control chromosomes in the GnomAD database, including 29,989 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 0.62 (29989 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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: 0.619 AC: 93966 AN: 151702 Hom.: 29940 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.620 AC: 94074 AN: 151820 Hom.: 29989 Cov.: 31 AF XY: 0.624 AC XY: 46315 AN XY: 74194

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.573

Alfa AF: 0.555 Hom.: 19278

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.1
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6582630; hg19: chr12-38743508;