21-42367392-C-T

Variant names:

• chr21-42367392-C-T
• rs35448902

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 0.13 in 151,938 control chromosomes in the GnomAD database, including 1,467 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 0.13 (1467 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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: 0.131 AC: 19813 AN: 151820 Hom.: 1470 Cov.: 30

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.130 AC: 19810 AN: 151938 Hom.: 1467 Cov.: 30 AF XY: 0.131 AC XY: 9747 AN XY: 74250

African (AFR) AF: 0.0816 AC: 3383 AN: 41436

American (AMR) AF: 0.104 AC: 1592 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3466

East Asian (EAS) AF: 0.228 AC: 1172 AN: 5138

South Asian (SAS) AF: 0.175 AC: 840 AN: 4810

European-Finnish (FIN) AF: 0.144 AC: 1515 AN: 10546

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10380 AN: 67956

Other (OTH) AF: 0.150 AC: 316 AN: 2104

Alfa AF: 0.145 Hom.: 2619

Bravo AF: 0.125

Asia WGS AF: 0.179 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.32
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs35448902; hg19: chr21-43787501;