14-65924381-G-A

Variant names:

• chr14-65924381-G-A
• rs2318308

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 0.344 in 151,706 control chromosomes in the GnomAD database, including 9,669 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 0.34 (9669 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.344 AC: 52166 AN: 151588 Hom.: 9646 Cov.: 30

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.344 AC: 52239 AN: 151706 Hom.: 9669 Cov.: 30 AF XY: 0.343 AC XY: 25469 AN XY: 74152

African (AFR) AF: 0.472 AC: 19498 AN: 41304

American (AMR) AF: 0.368 AC: 5616 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1150 AN: 3464

East Asian (EAS) AF: 0.272 AC: 1401 AN: 5152

South Asian (SAS) AF: 0.269 AC: 1291 AN: 4798

European-Finnish (FIN) AF: 0.251 AC: 2632 AN: 10492

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19521 AN: 67914

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.307 Hom.: 25262

Bravo AF: 0.361

Asia WGS AF: 0.321 AC: 1117 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.49
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2318308; hg19: chr14-66391099;