chr4-102101892-T-C

Variant names:

• chr4-102101892-T-C
• rs173218

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 0.765 in 151,968 control chromosomes in the GnomAD database, including 44,880 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 0.76 (44880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116158 AN: 151844 Hom.: 44853 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.765 AC: 116237 AN: 151968 Hom.: 44880 Cov.: 32 AF XY: 0.763 AC XY: 56671 AN XY: 74296

African (AFR) AF: 0.682 AC: 28255 AN: 41440

American (AMR) AF: 0.712 AC: 10857 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2572 AN: 3466

East Asian (EAS) AF: 0.686 AC: 3542 AN: 5166

South Asian (SAS) AF: 0.823 AC: 3979 AN: 4832

European-Finnish (FIN) AF: 0.839 AC: 8881 AN: 10584

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.819 AC: 55615 AN: 67914

Other (OTH) AF: 0.749 AC: 1581 AN: 2112

Alfa AF: 0.805 Hom.: 35530

Bravo AF: 0.749

Asia WGS AF: 0.733 AC: 2547 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs173218; hg19: chr4-103023049;