rs1557361

Positions:

• chr21-44998900-T-C
• chr21-44998900-T-G

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 0.368 in 152,152 control chromosomes in the GnomAD database, including 13,085 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 0.37 (13085 hom., cov: 35)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44998900T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55841 AN: 152034 Hom.: 13059 Cov.: 35

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.368 AC: 55922 AN: 152152 Hom.: 13085 Cov.: 35 AF XY: 0.365 AC XY: 27142 AN XY: 74386

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.340

Alfa AF: 0.309 Hom.: 1189

Bravo AF: 0.394

Asia WGS AF: 0.304 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557361; hg19: chr21-46418814;