20-41890348-C-T

Variant names:

• chr20-41890348-C-T
• rs10485682

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 0.0195 in 151,974 control chromosomes in the GnomAD database, including 138 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 0.020 (138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0195 AC: 2965 AN: 151858 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.00538

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.00464

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00459

Gnomad OTH AF: 0.0317

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

GnomAD4 genome AF: 0.0195 AC: 2964 AN: 151974 Hom.: 138 Cov.: 32 AF XY: 0.0208 AC XY: 1546 AN XY: 74276

African (AFR) AF: 0.00536 AC: 222 AN: 41412

American (AMR) AF: 0.0958 AC: 1461 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.138 AC: 711 AN: 5170

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4816

European-Finnish (FIN) AF: 0.00464 AC: 49 AN: 10562

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00459 AC: 312 AN: 67986

Other (OTH) AF: 0.0304 AC: 64 AN: 2106

Alfa AF: 0.0139 Hom.: 103

Bravo AF: 0.0308

Asia WGS AF: 0.0660 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.72
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10485682; hg19: chr20-40518988;