rs1034120

Variant names:

• chr21-16824603-C-T
• rs1034120

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.214 in 152,068 control chromosomes in the GnomAD database, including 3,745 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 0.21 (3745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 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: 0.214 AC: 32465 AN: 151950 Hom.: 3737 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.214 AC: 32490 AN: 152068 Hom.: 3745 Cov.: 32 AF XY: 0.216 AC XY: 16035 AN XY: 74344

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.218

Alfa AF: 0.228 Hom.: 5065

Bravo AF: 0.218

Asia WGS AF: 0.280 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1034120; hg19: chr21-18196922;