rs2619538

Variant names:

• chr6-15664978-A-T
• rs2619538

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 0.529 in 152,106 control chromosomes in the GnomAD database, including 22,520 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 0.53 (22520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 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: 0.529 AC: 80439 AN: 151988 Hom.: 22515 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.529 AC: 80488 AN: 152106 Hom.: 22520 Cov.: 32 AF XY: 0.515 AC XY: 38307 AN XY: 74370

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.521

Alfa AF: 0.530 Hom.: 2699

Bravo AF: 0.542

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2619538; hg19: chr6-15665209;