chr14-75347325-T-C

Variant names:

• chr14-75347325-T-C
• rs11621969

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 0.144 in 152,274 control chromosomes in the GnomAD database, including 2,014 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 0.14 (2014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.144 AC: 21845 AN: 152156 Hom.: 2004 Cov.: 32

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.144 AC: 21862 AN: 152274 Hom.: 2014 Cov.: 32 AF XY: 0.148 AC XY: 10994 AN XY: 74450

Gnomad4 AFR AF: 0.0416

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.130

Alfa AF: 0.151 Hom.: 263

Bravo AF: 0.145

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11621969; hg19: chr14-75814028;