rs268923

Variant names:

• chr19-50918960-A-T
• rs268923

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 0.567 in 151,846 control chromosomes in the GnomAD database, including 25,184 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 0.57 (25184 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.635 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: 0.567 AC: 86100 AN: 151728 Hom.: 25163 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86171 AN: 151846 Hom.: 25184 Cov.: 31 AF XY: 0.566 AC XY: 42029 AN XY: 74202

African (AFR) AF: 0.549 AC: 22723 AN: 41378

American (AMR) AF: 0.646 AC: 9851 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2430 AN: 3468

East Asian (EAS) AF: 0.103 AC: 533 AN: 5160

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4808

European-Finnish (FIN) AF: 0.594 AC: 6251 AN: 10520

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40237 AN: 67952

Other (OTH) AF: 0.590 AC: 1243 AN: 2108

Alfa AF: 0.587 Hom.: 3297

Bravo AF: 0.570

Asia WGS AF: 0.312 AC: 1087 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs268923; hg19: chr19-51422216;