rs900400

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;