chr14-100649196-G-A

Variant names:

• chr14-100649196-G-A
• rs7160413

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 0.0848 in 152,194 control chromosomes in the GnomAD database, including 607 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 0.085 (607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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: 0.0848 AC: 12892 AN: 152076 Hom.: 606 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0848 AC: 12902 AN: 152194 Hom.: 607 Cov.: 33 AF XY: 0.0872 AC XY: 6488 AN XY: 74424

African (AFR) AF: 0.100 AC: 4170 AN: 41504

American (AMR) AF: 0.0518 AC: 793 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5178

South Asian (SAS) AF: 0.148 AC: 714 AN: 4830

European-Finnish (FIN) AF: 0.106 AC: 1126 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0793 AC: 5390 AN: 68000

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0853 Hom.: 353

Bravo AF: 0.0781

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.74
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7160413; hg19: chr14-101115533;