4-105490602-T-G

Variant names:

• chr4-105490602-T-G
• rs765220

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.800 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

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.809

Alfa AF: 0.738 Hom.: 1448

Bravo AF: 0.790

Asia WGS AF: 0.706 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765220; hg19: chr4-106411759;