chr14-40575322-T-C

Position:

• chr14-40575322-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 0.275 in 151,820 control chromosomes in the GnomAD database, including 5,914 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 0.28 (5914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.275 AC: 41715 AN: 151702 Hom.: 5910 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.275 AC: 41751 AN: 151820 Hom.: 5914 Cov.: 32 AF XY: 0.270 AC XY: 19993 AN XY: 74168

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.248

Alfa AF: 0.246 Hom.: 2178

Bravo AF: 0.276

Asia WGS AF: 0.232 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2415621; hg19: chr14-41044527;