rs901123

Variant names:

• chr4-20049110-G-A
• rs901123

Your query was ambiguous. Multiple possible variants found:

• chr4-20049110-G-A
• chr4-20049110-G-T

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 0.391 in 151,762 control chromosomes in the GnomAD database, including 11,947 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 0.39 (11947 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.391 AC: 59366 AN: 151646 Hom.: 11930 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.391 AC: 59413 AN: 151762 Hom.: 11947 Cov.: 31 AF XY: 0.388 AC XY: 28742 AN XY: 74154

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.379

Alfa AF: 0.339 Hom.: 8206

Bravo AF: 0.402

Asia WGS AF: 0.409 AC: 1422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs901123; hg19: chr4-20050733;