chr5-148024718-G-A

Position:

• chr5-148024718-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 0.437 in 151,870 control chromosomes in the GnomAD database, including 15,140 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 0.44 (15140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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 (AMR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66305 AN: 151752 Hom.: 15138 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.437 AC: 66315 AN: 151870 Hom.: 15140 Cov.: 32 AF XY: 0.442 AC XY: 32833 AN XY: 74216

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.467

Alfa AF: 0.468 Hom.: 33821

Bravo AF: 0.438

Asia WGS AF: 0.520 AC: 1802 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	1.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10477360; hg19: chr5-147404281;