chr14-65810939-G-A

Position:

• chr14-65810939-G-A

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 0.366 in 152,056 control chromosomes in the GnomAD database, including 11,289 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 0.37 (11289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 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: 0.366 AC: 55576 AN: 151936 Hom.: 11288 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.366 AC: 55605 AN: 152056 Hom.: 11289 Cov.: 33 AF XY: 0.373 AC XY: 27747 AN XY: 74338

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.374

Alfa AF: 0.420 Hom.: 26796

Bravo AF: 0.342

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10149555; hg19: chr14-66277657;