chr14-95613538-A-G

Variant names:

• chr14-95613538-A-G
• rs1885418

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 0.585 in 152,146 control chromosomes in the GnomAD database, including 27,069 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 0.59 (27069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.585 AC: 88988 AN: 152026 Hom.: 27045 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.585 AC: 89053 AN: 152146 Hom.: 27069 Cov.: 32 AF XY: 0.582 AC XY: 43257 AN XY: 74368

African (AFR) AF: 0.475 AC: 19717 AN: 41478

American (AMR) AF: 0.621 AC: 9503 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2225 AN: 3470

East Asian (EAS) AF: 0.186 AC: 963 AN: 5174

South Asian (SAS) AF: 0.428 AC: 2060 AN: 4818

European-Finnish (FIN) AF: 0.656 AC: 6945 AN: 10590

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45461 AN: 67998

Other (OTH) AF: 0.591 AC: 1250 AN: 2114

Alfa AF: 0.623 Hom.: 13783

Bravo AF: 0.576

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.77
DANN	Benign	0.66
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1885418; hg19: chr14-96079875;