rs741864

Variant names:

• chr21-39835868-G-A
• rs741864

Your query was ambiguous. Multiple possible variants found:

• chr21-39835868-G-A
• chr21-39835868-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.310 AC: 12839 AN: 41468

American (AMR) AF: 0.111 AC: 1702 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.111 AC: 572 AN: 5176

South Asian (SAS) AF: 0.102 AC: 493 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1072 AN: 10570

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7342 AN: 67994

Other (OTH) AF: 0.167 AC: 353 AN: 2112

Alfa AF: 0.122 Hom.: 4494

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs741864; hg19: chr21-41207795;