5-148816443-A-G

Variant names:

• chr5-148816443-A-G
• rs30297

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 0.9 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.974 AC: 40385 AN: 41482

American (AMR) AF: 0.827 AC: 12630 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3323 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5135 AN: 5176

South Asian (SAS) AF: 0.962 AC: 4639 AN: 4824

European-Finnish (FIN) AF: 0.858 AC: 9075 AN: 10572

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58844 AN: 67984

Other (OTH) AF: 0.901 AC: 1903 AN: 2112

Alfa AF: 0.909 Hom.: 24255

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs30297; hg19: chr5-148196006;