rs11623728

Variant names:

• chr14-97346319-G-A
• rs11623728

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 0.188 in 152,018 control chromosomes in the GnomAD database, including 3,365 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 0.19 (3365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 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: 0.188 AC: 28610 AN: 151900 Hom.: 3367 Cov.: 32

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.188 AC: 28610 AN: 152018 Hom.: 3365 Cov.: 32 AF XY: 0.191 AC XY: 14152 AN XY: 74270

Gnomad4 AFR AF: 0.0501

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.194

Alfa AF: 0.224 Hom.: 1017

Bravo AF: 0.175

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11623728; hg19: chr14-97812656;