rs7143583

Variant names:

• chr14-44845780-G-A
• rs7143583

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.147 in 152,098 control chromosomes in the GnomAD database, including 1,860 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 (1860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.147 AC: 22288 AN: 151980 Hom.: 1859 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.147 AC: 22313 AN: 152098 Hom.: 1860 Cov.: 32 AF XY: 0.146 AC XY: 10895 AN XY: 74370

Gnomad4 AFR AF: 0.0747

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.185

Alfa AF: 0.180 Hom.: 5361

Bravo AF: 0.149

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	7.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7143583; hg19: chr14-45314983;