5-123948785-C-T

Variant names:

• chr5-123948785-C-T
• rs330451

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 0.889 in 152,158 control chromosomes in the GnomAD database, including 60,488 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 0.89 (60488 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 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: 0.889 AC: 135220 AN: 152040 Hom.: 60440 Cov.: 31

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.889 AC: 135320 AN: 152158 Hom.: 60488 Cov.: 31 AF XY: 0.887 AC XY: 65982 AN XY: 74374

African (AFR) AF: 0.967 AC: 40170 AN: 41540

American (AMR) AF: 0.837 AC: 12791 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3267 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3828 AN: 5152

South Asian (SAS) AF: 0.932 AC: 4487 AN: 4816

European-Finnish (FIN) AF: 0.826 AC: 8742 AN: 10586

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

European-Non Finnish (NFE) AF: 0.869 AC: 59122 AN: 67998

Other (OTH) AF: 0.878 AC: 1855 AN: 2112

Alfa AF: 0.879 Hom.: 7307

Bravo AF: 0.890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs330451; hg19: chr5-123284479;