5-143255143-T-G

Variant names:

• chr5-143255143-T-G
• rs864354

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 0.467 in 151,936 control chromosomes in the GnomAD database, including 17,495 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 0.47 (17495 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 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: 0.467 AC: 70951 AN: 151818 Hom.: 17488 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.467 AC: 70993 AN: 151936 Hom.: 17495 Cov.: 31 AF XY: 0.460 AC XY: 34184 AN XY: 74274

African (AFR) AF: 0.350 AC: 14496 AN: 41420

American (AMR) AF: 0.390 AC: 5949 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1476 AN: 5164

South Asian (SAS) AF: 0.404 AC: 1948 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5357 AN: 10514

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38303 AN: 67972

Other (OTH) AF: 0.462 AC: 977 AN: 2114

Alfa AF: 0.530 Hom.: 10951

Bravo AF: 0.454

Asia WGS AF: 0.376 AC: 1308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs864354; hg19: chr5-142634708;