chr5-122100901-C-T

Variant names:

• chr5-122100901-C-T
• rs890749

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 0.85 in 152,224 control chromosomes in the GnomAD database, including 55,381 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 0.85 (55381 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129284 AN: 152106 Hom.: 55316 Cov.: 33

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.850 AC: 129407 AN: 152224 Hom.: 55381 Cov.: 33 AF XY: 0.852 AC XY: 63446 AN XY: 74426

African (AFR) AF: 0.949 AC: 39458 AN: 41560

American (AMR) AF: 0.827 AC: 12642 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2652 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4430 AN: 5172

South Asian (SAS) AF: 0.841 AC: 4052 AN: 4818

European-Finnish (FIN) AF: 0.845 AC: 8946 AN: 10592

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.800 AC: 54399 AN: 68006

Other (OTH) AF: 0.820 AC: 1734 AN: 2114

Alfa AF: 0.825 Hom.: 84749

Bravo AF: 0.849

Asia WGS AF: 0.887 AC: 3087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.041
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs890749; hg19: chr5-121436596;