5-74554158-T-G

Variant names:

• chr5-74554158-T-G
• rs298387

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 0.342 in 152,036 control chromosomes in the GnomAD database, including 9,334 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 0.34 (9334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.438 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52024 AN: 151918 Hom.: 9327 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.342 AC: 52056 AN: 152036 Hom.: 9334 Cov.: 32 AF XY: 0.339 AC XY: 25200 AN XY: 74334

African (AFR) AF: 0.444 AC: 18378 AN: 41426

American (AMR) AF: 0.253 AC: 3866 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1448 AN: 5176

South Asian (SAS) AF: 0.307 AC: 1477 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3507 AN: 10586

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21188 AN: 67968

Other (OTH) AF: 0.331 AC: 699 AN: 2112

Alfa AF: 0.335 Hom.: 1057

Bravo AF: 0.339

Asia WGS AF: 0.316 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.47
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs298387; hg19: chr5-73849983;