rs3021304

Variant names:

• chr6-32607881-G-C
• rs3021304

Your query was ambiguous. Multiple possible variants found:

• chr6-32607881-G-C
• chr6-32607881-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 0.514 in 150,450 control chromosomes in the GnomAD database, including 20,448 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 (20448 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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: 77242 AN: 150332 Hom.: 20428 Cov.: 29

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.514 AC: 77312 AN: 150450 Hom.: 20448 Cov.: 29 AF XY: 0.516 AC XY: 37905 AN XY: 73476

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.525

Alfa AF: 0.511 Hom.: 2231

Bravo AF: 0.511

Asia WGS AF: 0.504 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0020
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3021304; hg19: chr6-32575658;