rs1961544

Positions:

• chr21-19544988-G-C
• chr21-19544988-G-T

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 0.143 in 152,112 control chromosomes in the GnomAD database, including 1,724 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 0.14 (1724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21759 AN: 151996 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.143 AC: 21778 AN: 152112 Hom.: 1724 Cov.: 32 AF XY: 0.145 AC XY: 10777 AN XY: 74328

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.127

Alfa AF: 0.140 Hom.: 191

Bravo AF: 0.134

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.3
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1961544; hg19: chr21-20917303;