rs4693018

chr4-82108522-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0123 in 148,248 control chromosomes in the GnomAD database, including 33 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 0.012 (33 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.72

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0123 (1830/148248) while in subpopulation AMR AF= 0.0395 (586/14854). AF 95% confidence interval is 0.0368. There are 33 homozygotes in gnomad4. There are 889 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 31 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0123 AC: 1825 AN: 148112 Hom.: 31 Cov.: 30

Gnomad AFR AF: 0.00391

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.00734

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.00440

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0161

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

GnomAD4 genome AF: 0.0123 AC: 1830 AN: 148248 Hom.: 33 Cov.: 30 AF XY: 0.0123 AC XY: 889 AN XY: 72280

Gnomad4 AFR AF: 0.00390

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.00734

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.00970

Gnomad4 FIN AF: 0.00440

Gnomad4 NFE AF: 0.0138

Gnomad4 OTH AF: 0.0159

Alfa AF: 0.0133 Hom.: 1

Bravo AF: 0.0154

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
Cadd	Benign	22
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4693018; hg19: chr4-83029675;