rs7146193

Variant names:

• chr14-88980452-A-G
• rs7146193

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 0.614 in 152,112 control chromosomes in the GnomAD database, including 29,110 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 0.61 (29110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.614 AC: 93272 AN: 151996 Hom.: 29077 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.614 AC: 93354 AN: 152112 Hom.: 29110 Cov.: 32 AF XY: 0.610 AC XY: 45341 AN XY: 74370

African (AFR) AF: 0.714 AC: 29627 AN: 41508

American (AMR) AF: 0.510 AC: 7795 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1899 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2492 AN: 5174

South Asian (SAS) AF: 0.517 AC: 2491 AN: 4818

European-Finnish (FIN) AF: 0.639 AC: 6759 AN: 10576

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.593 AC: 40309 AN: 67974

Other (OTH) AF: 0.600 AC: 1268 AN: 2114

Alfa AF: 0.592 Hom.: 119322

Bravo AF: 0.608

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs7146193; hg19: chr14-89446796;