22-19750098-T-C

Variant names:

• chr22-19750098-T-C
• rs5993820

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 0.668 in 151,958 control chromosomes in the GnomAD database, including 34,059 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 0.67 (34059 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101433 AN: 151840 Hom.: 34024 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.668 AC: 101528 AN: 151958 Hom.: 34059 Cov.: 33 AF XY: 0.664 AC XY: 49324 AN XY: 74248

African (AFR) AF: 0.725 AC: 30067 AN: 41448

American (AMR) AF: 0.637 AC: 9736 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3468

East Asian (EAS) AF: 0.581 AC: 3002 AN: 5164

South Asian (SAS) AF: 0.701 AC: 3384 AN: 4824

European-Finnish (FIN) AF: 0.585 AC: 6169 AN: 10554

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.658 AC: 44672 AN: 67908

Other (OTH) AF: 0.657 AC: 1387 AN: 2110

Alfa AF: 0.665 Hom.: 63708

Bravo AF: 0.674

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.41
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs5993820; hg19: chr22-19737621; COSMIC: COSV60107268;