rs624968

Variant names:

• chr19-6623877-C-G
• rs624968

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.580 AC: 24067 AN: 41476

American (AMR) AF: 0.393 AC: 5996 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4290 AN: 5182

South Asian (SAS) AF: 0.426 AC: 2056 AN: 4826

European-Finnish (FIN) AF: 0.413 AC: 4367 AN: 10562

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31392 AN: 67980

Other (OTH) AF: 0.477 AC: 1007 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.45
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs624968; hg19: chr19-6623888;