chr14-20846841-C-T

Variant names:

• chr14-20846841-C-T
• rs11622895

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 0.493 in 151,944 control chromosomes in the GnomAD database, including 19,556 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 (19556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 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: 0.493 AC: 74845 AN: 151826 Hom.: 19550 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.493 AC: 74868 AN: 151944 Hom.: 19556 Cov.: 31 AF XY: 0.496 AC XY: 36880 AN XY: 74280

African (AFR) AF: 0.321 AC: 13290 AN: 41450

American (AMR) AF: 0.596 AC: 9105 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1943 AN: 5150

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4810

European-Finnish (FIN) AF: 0.583 AC: 6144 AN: 10544

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39135 AN: 67932

Other (OTH) AF: 0.472 AC: 997 AN: 2112

Alfa AF: 0.543 Hom.: 84515

Bravo AF: 0.486

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.72
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11622895; hg19: chr14-21315000;