rs3918240

Variant names:

• chr20-46006977-C-T
• rs3918240

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 0.355 in 151,980 control chromosomes in the GnomAD database, including 10,177 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 0.35 (10177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.355 AC: 53898 AN: 151862 Hom.: 10175 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.355 AC: 53926 AN: 151980 Hom.: 10177 Cov.: 32 AF XY: 0.361 AC XY: 26800 AN XY: 74272

African (AFR) AF: 0.309 AC: 12795 AN: 41436

American (AMR) AF: 0.270 AC: 4129 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3749 AN: 5168

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4814

European-Finnish (FIN) AF: 0.417 AC: 4391 AN: 10532

Middle Eastern (MID) AF: 0.345 AC: 100 AN: 290

European-Non Finnish (NFE) AF: 0.356 AC: 24203 AN: 67980

Other (OTH) AF: 0.344 AC: 725 AN: 2110

Alfa AF: 0.354 Hom.: 36436

Bravo AF: 0.342

Asia WGS AF: 0.527 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs3918240; hg19: chr20-44635616;