chr4-105490602-T-G

Variant names:

• chr4-105490602-T-G
• rs765220

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 0.799 in 151,164 control chromosomes in the GnomAD database, including 48,570 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 0.80 (48570 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 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: 0.800 AC: 120768 AN: 151046 Hom.: 48556 Cov.: 28

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.799 AC: 120831 AN: 151164 Hom.: 48570 Cov.: 28 AF XY: 0.796 AC XY: 58814 AN XY: 73852

African (AFR) AF: 0.741 AC: 30425 AN: 41054

American (AMR) AF: 0.771 AC: 11722 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2745 AN: 3460

East Asian (EAS) AF: 0.574 AC: 2944 AN: 5128

South Asian (SAS) AF: 0.840 AC: 4014 AN: 4776

European-Finnish (FIN) AF: 0.828 AC: 8656 AN: 10456

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57581 AN: 67784

Other (OTH) AF: 0.809 AC: 1701 AN: 2102

Alfa AF: 0.752 Hom.: 5649

Bravo AF: 0.790

Asia WGS AF: 0.706 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.11
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs765220; hg19: chr4-106411759;