chr14-20489331-T-G

Variant names:

• chr14-20489331-T-G
• rs17112431

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 0.18 in 152,140 control chromosomes in the GnomAD database, including 2,584 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 0.18 (2584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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: 0.180 AC: 27412 AN: 152022 Hom.: 2580 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.180 AC: 27424 AN: 152140 Hom.: 2584 Cov.: 32 AF XY: 0.177 AC XY: 13193 AN XY: 74390

African (AFR) AF: 0.190 AC: 7865 AN: 41492

American (AMR) AF: 0.162 AC: 2469 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3470

East Asian (EAS) AF: 0.00579 AC: 30 AN: 5184

South Asian (SAS) AF: 0.124 AC: 601 AN: 4828

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10580

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12602 AN: 67988

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.168 Hom.: 812

Bravo AF: 0.180

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.4
DANN	Benign	0.69
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs17112431; hg19: chr14-20957490;