rs3955261

Variant names:

• chr4-179833869-G-A
• rs3955261

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 0.196 in 152,024 control chromosomes in the GnomAD database, including 3,131 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 0.20 (3131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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: 0.196 AC: 29827 AN: 151906 Hom.: 3126 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.196 AC: 29857 AN: 152024 Hom.: 3131 Cov.: 32 AF XY: 0.193 AC XY: 14312 AN XY: 74290

African (AFR) AF: 0.192 AC: 7954 AN: 41474

American (AMR) AF: 0.156 AC: 2384 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3468

East Asian (EAS) AF: 0.0291 AC: 150 AN: 5156

South Asian (SAS) AF: 0.158 AC: 762 AN: 4812

European-Finnish (FIN) AF: 0.201 AC: 2126 AN: 10556

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15138 AN: 67966

Other (OTH) AF: 0.207 AC: 437 AN: 2112

Alfa AF: 0.212 Hom.: 603

Bravo AF: 0.192

Asia WGS AF: 0.115 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.77
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs3955261; hg19: chr4-180755022;