5-25914923-A-G

Variant names:

• chr5-25914923-A-G
• rs7447989

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 0.327 in 151,870 control chromosomes in the GnomAD database, including 8,824 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 0.33 (8824 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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: 0.327 AC: 49695 AN: 151752 Hom.: 8828 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.327 AC: 49711 AN: 151870 Hom.: 8824 Cov.: 32 AF XY: 0.331 AC XY: 24597 AN XY: 74210

African (AFR) AF: 0.200 AC: 8306 AN: 41444

American (AMR) AF: 0.371 AC: 5659 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3466

East Asian (EAS) AF: 0.603 AC: 3109 AN: 5156

South Asian (SAS) AF: 0.463 AC: 2231 AN: 4816

European-Finnish (FIN) AF: 0.332 AC: 3505 AN: 10550

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24619 AN: 67858

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.331 Hom.: 4436

Bravo AF: 0.320

Asia WGS AF: 0.493 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.63
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs7447989; hg19: chr5-25915032;