rs6582630

Variant names:

• chr12-38349706-G-A
• rs6582630

Your query was ambiguous. Multiple possible variants found:

• chr12-38349706-G-A
• chr12-38349706-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;