rs1961544

Variant names:

• chr21-19544988-G-C
• rs1961544

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;