rs2523477

Variant names:

• chr6-31392612-T-C
• rs2523477

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 0.102 in 151,824 control chromosomes in the GnomAD database, including 1,207 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 0.10 (1207 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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: 0.102 AC: 15486 AN: 151706 Hom.: 1204 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0722

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00773

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.102 AC: 15502 AN: 151824 Hom.: 1207 Cov.: 31 AF XY: 0.0985 AC XY: 7314 AN XY: 74226

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0722

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.00773

Gnomad4 NFE AF: 0.0795

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0845 Hom.: 499

Bravo AF: 0.118

Asia WGS AF: 0.0700 AC: 241 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523477; hg19: chr6-31360389;