chr14-94839675-C-A

Variant names:

• chr14-94839675-C-A
• rs11624318

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 0.148 in 152,068 control chromosomes in the GnomAD database, including 2,187 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 0.15 (2187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22507 AN: 151950 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.148 AC: 22512 AN: 152068 Hom.: 2187 Cov.: 32 AF XY: 0.150 AC XY: 11140 AN XY: 74316

African (AFR) AF: 0.0374 AC: 1552 AN: 41536

American (AMR) AF: 0.130 AC: 1992 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3470

East Asian (EAS) AF: 0.128 AC: 661 AN: 5172

South Asian (SAS) AF: 0.108 AC: 521 AN: 4806

European-Finnish (FIN) AF: 0.282 AC: 2978 AN: 10548

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13922 AN: 67960

Other (OTH) AF: 0.133 AC: 281 AN: 2106

Alfa AF: 0.183 Hom.: 4599

Bravo AF: 0.131

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.029
DANN	Benign	0.48
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11624318; hg19: chr14-95306012;