14-23035574-A-G

Variant names:

• chr14-23035574-A-G
• rs8020463

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 0.538 in 152,070 control chromosomes in the GnomAD database, including 25,804 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 0.54 (25804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.537 AC: 81662 AN: 151954 Hom.: 25741 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.538 AC: 81766 AN: 152070 Hom.: 25804 Cov.: 32 AF XY: 0.530 AC XY: 39421 AN XY: 74326

African (AFR) AF: 0.889 AC: 36915 AN: 41514

American (AMR) AF: 0.365 AC: 5568 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1036 AN: 5180

South Asian (SAS) AF: 0.483 AC: 2324 AN: 4816

European-Finnish (FIN) AF: 0.403 AC: 4261 AN: 10566

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28629 AN: 67956

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

Alfa AF: 0.448 Hom.: 7662

Bravo AF: 0.547

Asia WGS AF: 0.388 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		0.48
PromoterAI		-0.0090	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8020463; hg19: chr14-23504783;