rs2523619

chr6-31350367-T-C

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 0.232 in 152,002 control chromosomes in the GnomAD database, including 4,341 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 0.23 (4341 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

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 (SAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35280 AN: 151884 Hom.: 4339 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.232 AC: 35303 AN: 152002 Hom.: 4341 Cov.: 31 AF XY: 0.234 AC XY: 17410 AN XY: 74312

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.270

Alfa AF: 0.215 Hom.: 5035

Bravo AF: 0.243

Asia WGS AF: 0.227 AC: 791 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	8.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523619; hg19: chr6-31318144;