4-107383042-G-T

Variant names:

• chr4-107383042-G-T
• rs7680468

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.025 in 152,266 control chromosomes in the GnomAD database, including 40 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 0.025 (40 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.025 (3814/152266) while in subpopulation EAS AF = 0.0396 (205/5182). AF 95% confidence interval is 0.0351. There are 40 homozygotes in GnomAd4. There are 1875 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0251 AC: 3814 AN: 152148 Hom.: 40 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0250 AC: 3814 AN: 152266 Hom.: 40 Cov.: 32 AF XY: 0.0252 AC XY: 1875 AN XY: 74450

African (AFR) AF: 0.0181 AC: 751 AN: 41532

American (AMR) AF: 0.0358 AC: 548 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3468

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5182

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4824

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0279 AC: 1901 AN: 68038

Other (OTH) AF: 0.0336 AC: 71 AN: 2112

Alfa AF: 0.0275 Hom.: 47

Bravo AF: 0.0267

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.65
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs7680468; hg19: chr4-108304199;