rs900400

Variant names:

• chr3-157080986-T-C
• rs900400

Your query was ambiguous. Multiple possible variants found:

• chr3-157080986-T-C
• chr3-157080986-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.365 in 152,188 control chromosomes in the GnomAD database, including 10,667 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 0.37 (10667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.365 AC: 55574 AN: 152070 Hom.: 10672 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.365 AC: 55589 AN: 152188 Hom.: 10667 Cov.: 33 AF XY: 0.361 AC XY: 26841 AN XY: 74408

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.409

Alfa AF: 0.416 Hom.: 5974

Bravo AF: 0.373

Asia WGS AF: 0.354 AC: 1226 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.5
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs900400; hg19: chr3-156798775;