rs2673925

Variant names:

• chr5-136369986-G-A
• rs2673925

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 0.377 in 151,898 control chromosomes in the GnomAD database, including 11,710 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 0.38 (11710 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.376 AC: 57127 AN: 151778 Hom.: 11675 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.377 AC: 57216 AN: 151898 Hom.: 11710 Cov.: 31 AF XY: 0.371 AC XY: 27529 AN XY: 74248

African (AFR) AF: 0.549 AC: 22725 AN: 41390

American (AMR) AF: 0.313 AC: 4779 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3464

East Asian (EAS) AF: 0.421 AC: 2161 AN: 5138

South Asian (SAS) AF: 0.208 AC: 996 AN: 4798

European-Finnish (FIN) AF: 0.303 AC: 3198 AN: 10562

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20781 AN: 67968

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.330 Hom.: 36871

Bravo AF: 0.394

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.33
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs2673925; hg19: chr5-135705674;