21-44998186-C-T

Variant names:

• chr21-44998186-C-T
• rs13048981

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 0.0655 in 152,304 control chromosomes in the GnomAD database, including 435 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 0.066 (435 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0936 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: 0.0656 AC: 9981 AN: 152186 Hom.: 434 Cov.: 34

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.0760

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0956

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0655 AC: 9978 AN: 152304 Hom.: 435 Cov.: 34 AF XY: 0.0625 AC XY: 4655 AN XY: 74474

African (AFR) AF: 0.0185 AC: 769 AN: 41570

American (AMR) AF: 0.0620 AC: 948 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3472

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5174

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4828

European-Finnish (FIN) AF: 0.0702 AC: 745 AN: 10620

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0956 AC: 6500 AN: 68020

Other (OTH) AF: 0.0756 AC: 160 AN: 2116

Alfa AF: 0.0375 Hom.: 34

Bravo AF: 0.0624

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.71
DANN	Benign	0.57
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs13048981; hg19: chr21-46418100;