chr14-97346319-G-A

Variant names:

• chr14-97346319-G-A
• rs11623728

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0501 AC: 2081 AN: 41502

American (AMR) AF: 0.193 AC: 2949 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3470

East Asian (EAS) AF: 0.124 AC: 638 AN: 5156

South Asian (SAS) AF: 0.312 AC: 1501 AN: 4806

European-Finnish (FIN) AF: 0.251 AC: 2650 AN: 10542

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17017 AN: 67962

Other (OTH) AF: 0.194 AC: 407 AN: 2098

Alfa AF: 0.222 Hom.: 1572

Bravo AF: 0.175

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs11623728; hg19: chr14-97812656;