rs2400642

Variant names:

• chr5-148735243-A-G
• rs2400642

Your query was ambiguous. Multiple possible variants found:

• chr5-148735243-A-G
• chr5-148735243-A-T

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 0.247 in 152,180 control chromosomes in the GnomAD database, including 4,805 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 0.25 (4805 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 8 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 = 0.436 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37490 AN: 152062 Hom.: 4801 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37526 AN: 152180 Hom.: 4805 Cov.: 33 AF XY: 0.246 AC XY: 18330 AN XY: 74408

African (AFR) AF: 0.263 AC: 10905 AN: 41520

American (AMR) AF: 0.285 AC: 4355 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2339 AN: 5182

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10588

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15260 AN: 68004

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.236 Hom.: 7487

Bravo AF: 0.258

Asia WGS AF: 0.336 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2400642; hg19: chr5-148114806;