rs624968

chr19-6623877-C-G

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 0.495 in 152,084 control chromosomes in the GnomAD database, including 19,276 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 0.49 (19276 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.495 AC: 75236 AN: 151966 Hom.: 19267 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.495 AC: 75281 AN: 152084 Hom.: 19276 Cov.: 33 AF XY: 0.492 AC XY: 36559 AN XY: 74332

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.477

Alfa AF: 0.482 Hom.: 2477

Bravo AF: 0.503

Asia WGS AF: 0.570 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
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: rs624968; hg19: chr19-6623888;