rs4669378

Variant names:

• chr2-9175354-T-C
• rs4669378

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 0.548 in 151,708 control chromosomes in the GnomAD database, including 23,590 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 0.55 (23590 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.548 AC: 83082 AN: 151588 Hom.: 23547 Cov.: 30

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.548 AC: 83175 AN: 151708 Hom.: 23590 Cov.: 30 AF XY: 0.552 AC XY: 40932 AN XY: 74122

African (AFR) AF: 0.683 AC: 28258 AN: 41344

American (AMR) AF: 0.495 AC: 7545 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1254 AN: 5152

South Asian (SAS) AF: 0.602 AC: 2890 AN: 4802

European-Finnish (FIN) AF: 0.573 AC: 6030 AN: 10528

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33601 AN: 67880

Other (OTH) AF: 0.528 AC: 1110 AN: 2104

Alfa AF: 0.513 Hom.: 10921

Bravo AF: 0.543

Asia WGS AF: 0.454 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.60
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4669378; hg19: chr2-9315483;