chr14-43616565-T-C

Position:

• chr14-43616565-T-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 0.243 in 152,020 control chromosomes in the GnomAD database, including 4,617 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 0.24 (4617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36972 AN: 151900 Hom.: 4617 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.243 AC: 36990 AN: 152020 Hom.: 4617 Cov.: 32 AF XY: 0.243 AC XY: 18055 AN XY: 74332

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.224

Alfa AF: 0.249 Hom.: 2300

Bravo AF: 0.239

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8011986; hg19: chr14-44085768;