14-106772332-C-T

Position:

• chr14-106772332-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00565 in 140,464 control chromosomes in the GnomAD database, including 6 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 0.0057 (6 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.106772332C>T		intergenic_region
IGH		n.106772332C>T		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00566 AC: 794 AN: 140350 Hom.: 6 Cov.: 27

Gnomad AFR AF: 0.00647

Gnomad AMI AF: 0.00235

Gnomad AMR AF: 0.00482

Gnomad ASJ AF: 0.00694

Gnomad EAS AF: 0.00516

Gnomad SAS AF: 0.00677

Gnomad FIN AF: 0.00563

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00515

Gnomad OTH AF: 0.0117

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

GnomAD4 genome AF: 0.00565 AC: 794 AN: 140464 Hom.: 6 Cov.: 27 AF XY: 0.00665 AC XY: 455 AN XY: 68456

Gnomad4 AFR AF: 0.00645

Gnomad4 AMR AF: 0.00482

Gnomad4 ASJ AF: 0.00694

Gnomad4 EAS AF: 0.00517

Gnomad4 SAS AF: 0.00677

Gnomad4 FIN AF: 0.00563

Gnomad4 NFE AF: 0.00515

Gnomad4 OTH AF: 0.0116

Alfa AF: 0.0308 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2337406; hg19: chr14-107180574;