rs984369

Variant names:

• chr4-133071026-A-C
• rs984369

Your query was ambiguous. Multiple possible variants found:

• chr4-133071026-A-C
• chr4-133071026-A-G

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 0.457 in 151,876 control chromosomes in the GnomAD database, including 15,965 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 0.46 (15965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 0 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 = 0.482 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: 0.457 AC: 69413 AN: 151756 Hom.: 15955 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.457 AC: 69455 AN: 151876 Hom.: 15965 Cov.: 32 AF XY: 0.454 AC XY: 33714 AN XY: 74212

African (AFR) AF: 0.488 AC: 20211 AN: 41414

American (AMR) AF: 0.482 AC: 7348 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1730 AN: 5152

South Asian (SAS) AF: 0.427 AC: 2053 AN: 4812

European-Finnish (FIN) AF: 0.407 AC: 4296 AN: 10550

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

European-Non Finnish (NFE) AF: 0.452 AC: 30718 AN: 67920

Other (OTH) AF: 0.437 AC: 920 AN: 2106

Alfa AF: 0.456 Hom.: 4391

Bravo AF: 0.467

Asia WGS AF: 0.368 AC: 1280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs984369; hg19: chr4-133992181;