rs184900

Variant names:

• chr3-6400933-G-A
• rs184900

Your query was ambiguous. Multiple possible variants found:

• chr3-6400933-G-A
• chr3-6400933-G-C

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 0.608 in 151,938 control chromosomes in the GnomAD database, including 30,402 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 0.61 (30402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 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: 0.608 AC: 92320 AN: 151818 Hom.: 30403 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.608 AC: 92342 AN: 151938 Hom.: 30402 Cov.: 31 AF XY: 0.613 AC XY: 45506 AN XY: 74234

African (AFR) AF: 0.339 AC: 14027 AN: 41384

American (AMR) AF: 0.690 AC: 10536 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2116 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4283 AN: 5130

South Asian (SAS) AF: 0.719 AC: 3463 AN: 4818

European-Finnish (FIN) AF: 0.766 AC: 8091 AN: 10562

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47825 AN: 67992

Other (OTH) AF: 0.591 AC: 1245 AN: 2108

Alfa AF: 0.564 Hom.: 1866

Bravo AF: 0.586

Asia WGS AF: 0.705 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.58
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs184900; hg19: chr3-6442620;