14-97377773-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.256 in 151,960 control chromosomes in the GnomAD database, including 5,129 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 0.26 (5129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38852 AN: 151842 Hom.: 5133 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.256 AC: 38882 AN: 151960 Hom.: 5129 Cov.: 32 AF XY: 0.253 AC XY: 18794 AN XY: 74270

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.285

Alfa AF: 0.241 Hom.: 4514

Bravo AF: 0.259

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	14
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7144551; hg19: chr14-97844110;