chr21-44995960-C-T

Variant names:

• chr21-44995960-C-T
• rs11700697

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 0.33 in 152,084 control chromosomes in the GnomAD database, including 9,889 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 0.33 (9889 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 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: 0.330 AC: 50211 AN: 151966 Hom.: 9893 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.330 AC: 50215 AN: 152084 Hom.: 9889 Cov.: 33 AF XY: 0.335 AC XY: 24940 AN XY: 74338

African (AFR) AF: 0.107 AC: 4452 AN: 41522

American (AMR) AF: 0.367 AC: 5612 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1014 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1959 AN: 5140

South Asian (SAS) AF: 0.481 AC: 2316 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5037 AN: 10586

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28589 AN: 67928

Other (OTH) AF: 0.347 AC: 734 AN: 2116

Alfa AF: 0.384 Hom.: 2410

Bravo AF: 0.309

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs11700697; hg19: chr21-46415875;