rs2318308

Positions:

• chr14-65924381-G-A
• chr14-65924381-G-C

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 0.344 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.338

Alfa AF: 0.301 Hom.: 10454

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2318308; hg19: chr14-66391099;