5-147854895-G-A

Position:

• chr5-147854895-G-A

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 0.49 in 152,026 control chromosomes in the GnomAD database, including 21,210 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 0.49 (21210 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74424 AN: 151908 Hom.: 21164 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.490 AC: 74532 AN: 152026 Hom.: 21210 Cov.: 33 AF XY: 0.486 AC XY: 36088 AN XY: 74300

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.479

Alfa AF: 0.397 Hom.: 2528

Bravo AF: 0.514

Asia WGS AF: 0.615 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1432982; hg19: chr5-147234458; COSMIC: COSV72842715;