6-31353033-A-G

Variant names:

• chr6-31353033-A-G
• rs2596503

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 0.837 in 152,108 control chromosomes in the GnomAD database, including 53,574 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 0.84 (53574 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.892 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: 0.837 AC: 127262 AN: 151990 Hom.: 53512 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.837 AC: 127383 AN: 152108 Hom.: 53574 Cov.: 31 AF XY: 0.841 AC XY: 62544 AN XY: 74376

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.888

Alfa AF: 0.833 Hom.: 98976

Bravo AF: 0.847

Asia WGS AF: 0.867 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596503; hg19: chr6-31320810;