rs4693018

Variant names:

• chr4-82108522-G-T
• rs4693018

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 33 gene

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: 0.0123 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

African (AFR) AF: 0.00390 AC: 159 AN: 40796

American (AMR) AF: 0.0395 AC: 586 AN: 14854

Ashkenazi Jewish (ASJ) AF: 0.00734 AC: 25 AN: 3404

East Asian (EAS) AF: 0.00233 AC: 11 AN: 4724

South Asian (SAS) AF: 0.00970 AC: 43 AN: 4434

European-Finnish (FIN) AF: 0.00440 AC: 43 AN: 9782

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0138 AC: 927 AN: 67000

Other (OTH) AF: 0.0159 AC: 33 AN: 2076

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
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs4693018; hg19: chr4-83029675;