rs7146149

Variant names:

• chr14-28489017-G-T
• rs7146149

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 0.24 in 152,104 control chromosomes in the GnomAD database, including 4,646 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 0.24 (4646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 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: 0.240 AC: 36529 AN: 151986 Hom.: 4642 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36536 AN: 152104 Hom.: 4646 Cov.: 32 AF XY: 0.239 AC XY: 17798 AN XY: 74350

African (AFR) AF: 0.156 AC: 6456 AN: 41510

American (AMR) AF: 0.243 AC: 3716 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3468

East Asian (EAS) AF: 0.167 AC: 866 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2772 AN: 10542

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19762 AN: 67980

Other (OTH) AF: 0.271 AC: 571 AN: 2108

Alfa AF: 0.275 Hom.: 1179

Bravo AF: 0.236

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs7146149; hg19: chr14-28958223;