rs3918278

Variant names:

• chr20-46007015-G-A
• rs3918278

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0174 in 152,292 control chromosomes in the GnomAD database, including 41 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 0.017 (41 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0174 (2656/152292) while in subpopulation SAS AF = 0.0253 (122/4816). AF 95% confidence interval is 0.0229. There are 41 homozygotes in GnomAd4. There are 1309 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 41 gene

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: 0.0175 AC: 2658 AN: 152174 Hom.: 41 Cov.: 32

Gnomad AFR AF: 0.00321

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.00896

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0174 AC: 2656 AN: 152292 Hom.: 41 Cov.: 32 AF XY: 0.0176 AC XY: 1309 AN XY: 74476

African (AFR) AF: 0.00320 AC: 133 AN: 41566

American (AMR) AF: 0.00895 AC: 137 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4816

European-Finnish (FIN) AF: 0.0508 AC: 539 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0238 AC: 1620 AN: 68022

Other (OTH) AF: 0.0166 AC: 35 AN: 2114

Alfa AF: 0.0225 Hom.: 21

Bravo AF: 0.0142

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.75
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs3918278; hg19: chr20-44635654;