rs2535331

Variant names:

• chr6-30848493-G-A
• rs2535331

Your query was ambiguous. Multiple possible variants found:

• chr6-30848493-G-A
• chr6-30848493-G-C
• chr6-30848493-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 0.28 in 152,084 control chromosomes in the GnomAD database, including 6,864 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 0.28 (6864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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: 0.281 AC: 42636 AN: 151968 Hom.: 6866 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.280 AC: 42645 AN: 152084 Hom.: 6864 Cov.: 32 AF XY: 0.282 AC XY: 20926 AN XY: 74320

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.279

Alfa AF: 0.343 Hom.: 6669

Bravo AF: 0.264

Asia WGS AF: 0.212 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2535331; hg19: chr6-30816270;