rs1003846

Variant names:

• chr22-49333141-C-T
• rs1003846

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 0.109 in 152,242 control chromosomes in the GnomAD database, including 1,553 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 0.11 (1553 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 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: 0.109 AC: 16630 AN: 152124 Hom.: 1554 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0915

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.109 AC: 16644 AN: 152242 Hom.: 1553 Cov.: 33 AF XY: 0.108 AC XY: 8030 AN XY: 74446

African (AFR) AF: 0.246 AC: 10212 AN: 41498

American (AMR) AF: 0.0666 AC: 1019 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0915 AC: 317 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0526 AC: 254 AN: 4828

European-Finnish (FIN) AF: 0.0547 AC: 580 AN: 10612

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0582 AC: 3961 AN: 68032

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.0854 Hom.: 117

Bravo AF: 0.115

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1003846; hg19: chr22-49729066;