rs4678922

Variant names:

• chr3-36981373-A-T
• rs4678922

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 0.398 in 151,610 control chromosomes in the GnomAD database, including 12,552 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 0.40 (12552 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 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: 0.398 AC: 60264 AN: 151490 Hom.: 12546 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.398 AC: 60290 AN: 151610 Hom.: 12552 Cov.: 31 AF XY: 0.390 AC XY: 28902 AN XY: 74048

African (AFR) AF: 0.365 AC: 15091 AN: 41292

American (AMR) AF: 0.408 AC: 6228 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3466

East Asian (EAS) AF: 0.0781 AC: 402 AN: 5144

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4798

European-Finnish (FIN) AF: 0.366 AC: 3843 AN: 10486

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30840 AN: 67868

Other (OTH) AF: 0.382 AC: 804 AN: 2104

Alfa AF: 0.415 Hom.: 1633

Bravo AF: 0.399

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4678922; hg19: chr3-37022864;