21-44835681-A-G

Variant names:

• chr21-44835681-A-G
• rs4818979

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 0.236 in 152,004 control chromosomes in the GnomAD database, including 4,609 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 0.24 (4609 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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: 0.236 AC: 35863 AN: 151884 Hom.: 4602 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.236 AC: 35899 AN: 152004 Hom.: 4609 Cov.: 32 AF XY: 0.238 AC XY: 17686 AN XY: 74288

African (AFR) AF: 0.174 AC: 7238 AN: 41488

American (AMR) AF: 0.325 AC: 4963 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2411 AN: 5146

South Asian (SAS) AF: 0.154 AC: 743 AN: 4814

European-Finnish (FIN) AF: 0.287 AC: 3037 AN: 10586

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15853 AN: 67910

Other (OTH) AF: 0.256 AC: 540 AN: 2110

Alfa AF: 0.234 Hom.: 11426

Bravo AF: 0.246

Asia WGS AF: 0.267 AC: 925 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4818979; hg19: chr21-46255596;