rs741864

chr21-39835868-G-Achr21-39835868-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 0.163 in 152,106 control chromosomes in the GnomAD database, including 2,583 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 0.16 (2583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

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 = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24770 AN: 151988 Hom.: 2573 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.163 AC: 24806 AN: 152106 Hom.: 2583 Cov.: 32 AF XY: 0.158 AC XY: 11755 AN XY: 74370

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.167

Alfa AF: 0.108 Hom.: 1990

Bravo AF: 0.171

Asia WGS AF: 0.133 AC: 465 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	0.25
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs741864; hg19: chr21-41207795;