chr5-148816443-A-G

Position:

• chr5-148816443-A-G

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 0.9 in 152,092 control chromosomes in the GnomAD database, including 61,822 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 0.90 (61822 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 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: 0.900 AC: 136765 AN: 151976 Hom.: 61765 Cov.: 30

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.900 AC: 136879 AN: 152092 Hom.: 61822 Cov.: 30 AF XY: 0.900 AC XY: 66899 AN XY: 74350

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.901

Alfa AF: 0.880 Hom.: 7291

Bravo AF: 0.901

Asia WGS AF: 0.974 AC: 3388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30297; hg19: chr5-148196006;